Add options to startup script

Complete the documentation Readme file
A pretty jupyter login
2025-11-26 09:47:20 +01:00 · 2025-11-25 13:05:27 +01:00 · 2025-11-25 13:00:02 +01:00
364 changed files with 460578 additions and 170869 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,8 @@
 /jupyterhub_volumes/shared
 /jupyterhub_volumes/jupyterhub
 /jupyterhub_volumes/caddy
+/jupyterhub_volumes/course/data/Genbank
+/jupyterhub_volumes/web/
 /**/.DS_Store
 /web_src/**/*.RData
 /web_src/**/*.pdf
@@ -11,3 +13,7 @@
 /.luarc.json
 /sandbox
 *.log
+ncbitaxo_*
+Readme_files
+Readme.html
+tmp.*
--- a/Readme.html
+++ b/Readme.html
@@ -0,0 +1,709 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
+
+<meta charset="utf-8">
+<meta name="generator" content="quarto-1.8.26">
+
+<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
+
+
+<title>readme</title>
+<style>
+code{white-space: pre-wrap;}
+span.smallcaps{font-variant: small-caps;}
+div.columns{display: flex; gap: min(4vw, 1.5em);}
+div.column{flex: auto; overflow-x: auto;}
+div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ul.task-list{list-style: none;}
+ul.task-list li input[type="checkbox"] {
+  width: 0.8em;
+  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  vertical-align: middle;
+}
+/* CSS for syntax highlighting */
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+div.sourceCode { margin: 1em 0; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+  }
+pre.numberSource { margin-left: 3em;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+</style>
+
+
+<script src="Readme_files/libs/clipboard/clipboard.min.js"></script>
+<script src="Readme_files/libs/quarto-html/quarto.js" type="module"></script>
+<script src="Readme_files/libs/quarto-html/tabsets/tabsets.js" type="module"></script>
+<script src="Readme_files/libs/quarto-html/axe/axe-check.js" type="module"></script>
+<script src="Readme_files/libs/quarto-html/popper.min.js"></script>
+<script src="Readme_files/libs/quarto-html/tippy.umd.min.js"></script>
+<script src="Readme_files/libs/quarto-html/anchor.min.js"></script>
+<link href="Readme_files/libs/quarto-html/tippy.css" rel="stylesheet">
+<link href="Readme_files/libs/quarto-html/quarto-syntax-highlighting-587c61ba64f3a5504c4d52d930310e48.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<script src="Readme_files/libs/bootstrap/bootstrap.min.js"></script>
+<link href="Readme_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
+<link href="Readme_files/libs/bootstrap/bootstrap-d6a003b94517c951b2d65075d42fb01b.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
+
+
+</head>
+
+<body class="fullcontent quarto-light">
+
+<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
+
+<main class="content" id="quarto-document-content">
+
+
+
+
+<section id="obijupyterhub---the-dna-metabarcoding-learning-server" class="level1">
+<h1>OBIJupyterHub - the DNA Metabarcoding Learning Server</h1>
+<section id="intended-use" class="level2">
+<h2 class="anchored" data-anchor-id="intended-use">Intended use</h2>
+<p>This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and <code>./start-jupyterhub.sh</code> takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at <code>http://localhost:8888</code>. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.</p>
+</section>
+<section id="prerequisites-with-quick-checks" class="level2">
+<h2 class="anchored" data-anchor-id="prerequisites-with-quick-checks">Prerequisites (with quick checks)</h2>
+<p>You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.</p>
+<ul>
+<li>macOS: install <a href="https://orbstack.dev/">OrbStack</a> (recommended) or Docker Desktop; both ship Docker Engine and Compose.</li>
+<li>Linux: install Docker Engine and the Compose plugin from your distribution (e.g., <code>sudo apt install docker.io docker-compose-plugin</code>) or from Docker’s official packages.</li>
+<li>Windows: install Docker Desktop with the WSL2 backend enabled.</li>
+<li>Quarto CLI: get installers from <a href="https://quarto.org/docs/get-started/" class="uri">https://quarto.org/docs/get-started/</a>.</li>
+<li>Python 3: any recent version is fine (only the standard library is used).</li>
+</ul>
+<p>Verify from a terminal; if a command is missing, install it before moving on:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> <span class="at">--version</span></span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> compose version    <span class="co"># or: docker-compose --version</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> <span class="at">--version</span></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="ex">python3</span> <span class="at">--version</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+<section id="how-the-startup-script-works" class="level2">
+<h2 class="anchored" data-anchor-id="how-the-startup-script-works">How the startup script works</h2>
+<p><code>./start-jupyterhub.sh</code> is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:</p>
+<ul>
+<li>creates the <code>jupyterhub_volumes/</code> tree (caddy, course, shared, users, web…)</li>
+<li>builds <code>jupyterhub-student</code> and <code>jupyterhub-hub</code> images</li>
+<li>renders the Quarto site from <code>web_src/</code>, generates PDF galleries and <code>pages.json</code>, and copies everything into <code>jupyterhub_volumes/web/</code></li>
+<li>runs <code>docker-compose up -d --remove-orphans</code></li>
+</ul>
+<p>You can tailor what it does with a few flags:</p>
+<ul>
+<li><code>--no-build</code> (or <code>--offline</code>): skip Docker image builds and reuse existing images (useful when offline).</li>
+<li><code>--force-rebuild</code>: rebuild images without cache.</li>
+<li><code>--stop-server</code>: stop the stack and remove student containers, then exit.</li>
+<li><code>--update-lectures</code>: rebuild the course website only (no Docker stop/start).</li>
+</ul>
+</section>
+<section id="installation-and-first-run" class="level2">
+<h2 class="anchored" data-anchor-id="installation-and-first-run">Installation and first run</h2>
+<ol type="1">
+<li>Clone the project:</li>
+</ol>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git</span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> OBIJupyterHub</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<ol start="2" type="1">
+<li>(Optional) glance at the structure you’ll populate:</li>
+</ol>
+<pre><code>OBIJupyterHub
+├── start-jupyterhub.sh                  - single entry point (build + render + start)
+├── obijupyterhub                        - Docker images and stack definitions
+│&nbsp;&nbsp; ├── docker-compose.yml
+│&nbsp;&nbsp; ├── Dockerfile
+│&nbsp;&nbsp; ├── Dockerfile.hub
+│&nbsp;&nbsp; └── jupyterhub_config.py
+├── jupyterhub_volumes                   - data persisted on the host
+│&nbsp;&nbsp; ├── course                           - read-only for students (notebooks, data, bin, R packages)
+│&nbsp;&nbsp; ├── shared                           - shared read/write space for everyone
+│&nbsp;&nbsp; ├── users                            - per-user persistent data
+│&nbsp;&nbsp; └── web                              - rendered course website
+└── web_src                              - Quarto sources for the course website</code></pre>
+<ol start="3" type="1">
+<li>Prepare course materials (optional before first run):</li>
+</ol>
+<ul>
+<li>Put notebooks, datasets, scripts, binaries, or PDFs for students under <code>jupyterhub_volumes/course/</code>. They will appear read-only at <code>/home/jovyan/work/course/</code>.</li>
+<li>For collaborative work, drop files in <code>jupyterhub_volumes/shared/</code> (read/write for all at <code>/home/jovyan/work/shared/</code>).</li>
+<li>Edit or add Quarto sources in <code>web_src/</code> to update the course website; the script will render them.</li>
+</ul>
+<ol start="4" type="1">
+<li>Start everything (build + render + launch):</li>
+</ol>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<ol start="5" type="1">
+<li><p>Access JupyterHub in a browser at <code>http://localhost:8888</code>.</p></li>
+<li><p>Stop the stack when you’re done (run from <code>obijupyterhub/</code>):</p></li>
+</ol>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<section id="operating-the-stack-one-command-a-few-options" class="level3">
+<h3 class="anchored" data-anchor-id="operating-the-stack-one-command-a-few-options">Operating the stack (one command, a few options)</h3>
+<ul>
+<li>Start or rebuild: <code>./start-jupyterhub.sh</code> (rebuilds images, regenerates the website, starts the stack).</li>
+<li>Start without rebuilding images (offline): <code>./start-jupyterhub.sh --no-build</code></li>
+<li>Force rebuild without cache: <code>./start-jupyterhub.sh --force-rebuild</code></li>
+<li>Stop only: <code>./start-jupyterhub.sh --stop-server</code></li>
+<li>Rebuild website only (no Docker stop/start): <code>./start-jupyterhub.sh --update-lectures</code></li>
+<li>Access at <code>http://localhost:8888</code> (students: any username / password <code>metabar2025</code>; admin: <code>admin</code> / <code>admin2025</code>).</li>
+<li>Check logs from <code>obijupyterhub/</code> with <code>docker-compose logs -f jupyterhub</code>.</li>
+<li>Stop with <code>docker-compose down</code> (from <code>obijupyterhub/</code>). Rerun <code>./start-jupyterhub.sh</code> to start again or after config changes.</li>
+</ul>
+</section>
+</section>
+<section id="managing-shared-data" class="level2">
+<h2 class="anchored" data-anchor-id="managing-shared-data">Managing shared data</h2>
+<p>Each student lands in <code>/home/jovyan/work/</code> with three key areas: their own files, a shared space, and a read-only course space. Everything under <code>work/</code> is persisted on the host in <code>jupyterhub_volumes</code>.</p>
+<pre><code>work/                             # Personal workspace root (persistent)
+├── [student files]               # Their own files and notebooks
+├── R_packages/                   # Personal R packages (writable by student)
+├── shared/                       # Shared workspace (read/write, shared with all)
+└── course/                       # Course files (read-only, managed by admin)
+    ├── R_packages/               # Shared R packages (read-only, installed by prof)
+    ├── bin/                      # Shared executables (in PATH)
+    └── [course materials]        # Your course files</code></pre>
+<p>R looks for packages in this order: personal <code>work/R_packages/</code>, then shared <code>work/course/R_packages/</code>, then system libraries. Because everything lives under <code>work/</code>, student files survive restarts.</p>
+<section id="user-accounts" class="level3">
+<h3 class="anchored" data-anchor-id="user-accounts">User Accounts</h3>
+<p>Defaults are defined in <code>obijupyterhub/docker-compose.yml</code>: admin (<code>admin</code> / <code>admin2025</code>) with write access to <code>course/</code>, and students (any username, password <code>metabar2025</code>) with read-only access to <code>course/</code>. Adjust <code>JUPYTERHUB_ADMIN_PASSWORD</code> and <code>JUPYTERHUB_PASSWORD</code> there, then rerun <code>./start-jupyterhub.sh</code>.</p>
+</section>
+<section id="installing-r-packages-admin-only" class="level3">
+<h3 class="anchored" data-anchor-id="installing-r-packages-admin-only">Installing R Packages (Admin Only)</h3>
+<p>From the host, install shared R packages into <code>course/R_packages/</code>:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install packages</span></span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="ex">tools/install_packages.sh</span> reshape2 plotly knitr</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>Students can install their own packages into their personal <code>work/R_packages/</code>:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install in personal library (each student has their own)</span></span>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'mypackage'</span>)  <span class="co"># Will install in work/R_packages/</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+<section id="using-r-packages-students" class="level3">
+<h3 class="anchored" data-anchor-id="using-r-packages-students">Using R Packages (Students)</h3>
+<p>Students simply load packages normally:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reshape2)  <span class="co"># R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system</span></span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(plotly)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>R automatically searches in this order:</p>
+<ol type="1">
+<li>Personal packages: <code>/home/jovyan/work/R_packages/</code> (R_LIBS_USER)</li>
+<li>Prof packages: <code>/home/jovyan/work/course/R_packages/</code> (R_LIBS_SITE)</li>
+<li>System packages</li>
+</ol>
+</section>
+<section id="list-available-packages" class="level3">
+<h3 class="anchored" data-anchor-id="list-available-packages">List Available Packages</h3>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># List all available packages (personal + course + system)</span></span>
+<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">installed.packages</span>()[,<span class="st">"Package"</span>]</span>
+<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Check personal packages</span></span>
+<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/R_packages"</span>)</span>
+<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Check course packages (installed by prof)</span></span>
+<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/course/R_packages"</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+<section id="deposit-or-retrieve-course-and-student-files" class="level3">
+<h3 class="anchored" data-anchor-id="deposit-or-retrieve-course-and-student-files">Deposit or retrieve course and student files</h3>
+<p>On the host, place course files in <code>jupyterhub_volumes/course/</code> (they appear read-only to students), shared files in <code>jupyterhub_volumes/shared/</code>, and collect student work from <code>jupyterhub_volumes/users/</code>.</p>
+</section>
+</section>
+<section id="user-management" class="level2">
+<h2 class="anchored" data-anchor-id="user-management">User Management</h2>
+<section id="option-1-predefined-user-list" class="level3">
+<h3 class="anchored" data-anchor-id="option-1-predefined-user-list">Option 1: Predefined User List</h3>
+<p>In <code>jupyterhub_config.py</code>, uncomment and modify:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb11"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allowed_users <span class="op">=</span> {<span class="st">'student1'</span>, <span class="st">'student2'</span>, <span class="st">'student3'</span>}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+<section id="option-2-allow-everyone-for-testing" class="level3">
+<h3 class="anchored" data-anchor-id="option-2-allow-everyone-for-testing">Option 2: Allow Everyone (for testing)</h3>
+<p>By default, the configuration allows any user:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb12"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allow_all <span class="op">=</span> <span class="va">True</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>⚠️ <strong>Warning</strong>: DummyAuthenticator is ONLY for local testing!</p>
+</section>
+</section>
+<section id="kernel-verification" class="level2">
+<h2 class="anchored" data-anchor-id="kernel-verification">Kernel Verification</h2>
+<p>Once logged in, create a new notebook and verify you have access to:</p>
+<ul>
+<li><strong>Python 3</strong> (default kernel)</li>
+<li><strong>R</strong> (R kernel)</li>
+<li><strong>Bash</strong> (bash kernel)</li>
+</ul>
+</section>
+<section id="customization-for-your-labs" class="level2">
+<h2 class="anchored" data-anchor-id="customization-for-your-labs">Customization for Your Labs</h2>
+<section id="add-additional-r-packages" class="level3">
+<h3 class="anchored" data-anchor-id="add-additional-r-packages">Add Additional R Packages</h3>
+<p>Modify the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb13"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">R</span> <span class="at">-e</span> <span class="st">"install.packages(c('your_package'), repos='http://cran.rstudio.com/')"</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
+</section>
+<section id="add-python-packages" class="level3">
+<h3 class="anchored" data-anchor-id="add-python-packages">Add Python Packages</h3>
+<p>Add to the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb14"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">pip</span> install numpy pandas matplotlib seaborn</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
+</section>
+<section id="change-port-if-8000-is-occupied" class="level3">
+<h3 class="anchored" data-anchor-id="change-port-if-8000-is-occupied">Change Port (if 8000 is occupied)</h3>
+<p>Modify in <code>docker-compose.yml</code>:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb15"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ports</span><span class="kw">:</span></span>
+<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> </span><span class="st">"8001:8000"</span><span class="co">  # Accessible on localhost:8001</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+</section>
+<section id="advantages-of-this-approach" class="level2">
+<h2 class="anchored" data-anchor-id="advantages-of-this-approach">Advantages of This Approach</h2>
+<p>✅ <strong>Everything in Docker</strong>: No need to install Python/JupyterHub on your computer<br>
+✅ <strong>Portable</strong>: Easy to deploy on another server<br>
+✅ <strong>Isolated</strong>: No pollution of your system environment<br>
+✅ <strong>Easy to Clean</strong>: A simple <code>docker-compose down</code> is enough<br>
+✅ <strong>Reproducible</strong>: Students will have exactly the same environment</p>
+</section>
+<section id="troubleshooting" class="level2">
+<h2 class="anchored" data-anchor-id="troubleshooting">Troubleshooting</h2>
+<ul>
+<li>Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify <code>/var/run/docker.sock</code> exists.</li>
+<li>Student containers do not start: check <code>docker-compose logs jupyterhub</code> and confirm the images exist with <code>docker images | grep jupyterhub-student</code>.</li>
+<li>Port conflict: change the published port in <code>docker-compose.yml</code>.</li>
+</ul>
+<p><strong>I want to start from scratch</strong>:</p>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb16"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="bu">pushd</span> obijupyterhub</span>
+<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down <span class="at">-v</span></span>
+<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> rmi jupyterhub-hub jupyterhub-student</span>
+<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="bu">popd</span></span>
+<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Then rebuild everything</span></span>
+<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+</section>
+</section>
+
+</main>
+<!-- /main column -->
+<script id="quarto-html-after-body" type="application/javascript">
+  window.document.addEventListener("DOMContentLoaded", function (event) {
+    const icon = "";
+    const anchorJS = new window.AnchorJS();
+    anchorJS.options = {
+      placement: 'right',
+      icon: icon
+    };
+    anchorJS.add('.anchored');
+    const isCodeAnnotation = (el) => {
+      for (const clz of el.classList) {
+        if (clz.startsWith('code-annotation-')) {                     
+          return true;
+        }
+      }
+      return false;
+    }
+    const onCopySuccess = function(e) {
+      // button target
+      const button = e.trigger;
+      // don't keep focus
+      button.blur();
+      // flash "checked"
+      button.classList.add('code-copy-button-checked');
+      var currentTitle = button.getAttribute("title");
+      button.setAttribute("title", "Copied!");
+      let tooltip;
+      if (window.bootstrap) {
+        button.setAttribute("data-bs-toggle", "tooltip");
+        button.setAttribute("data-bs-placement", "left");
+        button.setAttribute("data-bs-title", "Copied!");
+        tooltip = new bootstrap.Tooltip(button, 
+          { trigger: "manual", 
+            customClass: "code-copy-button-tooltip",
+            offset: [0, -8]});
+        tooltip.show();    
+      }
+      setTimeout(function() {
+        if (tooltip) {
+          tooltip.hide();
+          button.removeAttribute("data-bs-title");
+          button.removeAttribute("data-bs-toggle");
+          button.removeAttribute("data-bs-placement");
+        }
+        button.setAttribute("title", currentTitle);
+        button.classList.remove('code-copy-button-checked');
+      }, 1000);
+      // clear code selection
+      e.clearSelection();
+    }
+    const getTextToCopy = function(trigger) {
+      const outerScaffold = trigger.parentElement.cloneNode(true);
+      const codeEl = outerScaffold.querySelector('code');
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+    }
+    const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+      text: getTextToCopy
+    });
+    clipboard.on('success', onCopySuccess);
+    if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+      const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
+        text: getTextToCopy,
+        container: window.document.getElementById('quarto-embedded-source-code-modal')
+      });
+      clipboardModal.on('success', onCopySuccess);
+    }
+      var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+      var mailtoRegex = new RegExp(/^mailto:/);
+        var filterRegex = new RegExp('/' + window.location.host + '/');
+      var isInternal = (href) => {
+          return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+      }
+      // Inspect non-navigation links and adorn them if external
+     var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
+      for (var i=0; i<links.length; i++) {
+        const link = links[i];
+        if (!isInternal(link.href)) {
+          // undo the damage that might have been done by quarto-nav.js in the case of
+          // links that we want to consider external
+          if (link.dataset.originalHref !== undefined) {
+            link.href = link.dataset.originalHref;
+          }
+        }
+      }
+    function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
+      const config = {
+        allowHTML: true,
+        maxWidth: 500,
+        delay: 100,
+        arrow: false,
+        appendTo: function(el) {
+            return el.parentElement;
+        },
+        interactive: true,
+        interactiveBorder: 10,
+        theme: 'quarto',
+        placement: 'bottom-start',
+      };
+      if (contentFn) {
+        config.content = contentFn;
+      }
+      if (onTriggerFn) {
+        config.onTrigger = onTriggerFn;
+      }
+      if (onUntriggerFn) {
+        config.onUntrigger = onUntriggerFn;
+      }
+      window.tippy(el, config); 
+    }
+    const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
+    for (var i=0; i<noterefs.length; i++) {
+      const ref = noterefs[i];
+      tippyHover(ref, function() {
+        // use id or data attribute instead here
+        let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
+        try { href = new URL(href).hash; } catch {}
+        const id = href.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note) {
+          return note.innerHTML;
+        } else {
+          return "";
+        }
+      });
+    }
+    const xrefs = window.document.querySelectorAll('a.quarto-xref');
+    const processXRef = (id, note) => {
+      // Strip column container classes
+      const stripColumnClz = (el) => {
+        el.classList.remove("page-full", "page-columns");
+        if (el.children) {
+          for (const child of el.children) {
+            stripColumnClz(child);
+          }
+        }
+      }
+      stripColumnClz(note)
+      if (id === null || id.startsWith('sec-')) {
+        // Special case sections, only their first couple elements
+        const container = document.createElement("div");
+        if (note.children && note.children.length > 2) {
+          container.appendChild(note.children[0].cloneNode(true));
+          for (let i = 1; i < note.children.length; i++) {
+            const child = note.children[i];
+            if (child.tagName === "P" && child.innerText === "") {
+              continue;
+            } else {
+              container.appendChild(child.cloneNode(true));
+              break;
+            }
+          }
+          if (window.Quarto?.typesetMath) {
+            window.Quarto.typesetMath(container);
+          }
+          return container.innerHTML
+        } else {
+          if (window.Quarto?.typesetMath) {
+            window.Quarto.typesetMath(note);
+          }
+          return note.innerHTML;
+        }
+      } else {
+        // Remove any anchor links if they are present
+        const anchorLink = note.querySelector('a.anchorjs-link');
+        if (anchorLink) {
+          anchorLink.remove();
+        }
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
+        if (note.classList.contains("callout")) {
+          return note.outerHTML;
+        } else {
+          return note.innerHTML;
+        }
+      }
+    }
+    for (var i=0; i<xrefs.length; i++) {
+      const xref = xrefs[i];
+      tippyHover(xref, undefined, function(instance) {
+        instance.disable();
+        let url = xref.getAttribute('href');
+        let hash = undefined; 
+        if (url.startsWith('#')) {
+          hash = url;
+        } else {
+          try { hash = new URL(url).hash; } catch {}
+        }
+        if (hash) {
+          const id = hash.replace(/^#\/?/, "");
+          const note = window.document.getElementById(id);
+          if (note !== null) {
+            try {
+              const html = processXRef(id, note.cloneNode(true));
+              instance.setContent(html);
+            } finally {
+              instance.enable();
+              instance.show();
+            }
+          } else {
+            // See if we can fetch this
+            fetch(url.split('#')[0])
+            .then(res => res.text())
+            .then(html => {
+              const parser = new DOMParser();
+              const htmlDoc = parser.parseFromString(html, "text/html");
+              const note = htmlDoc.getElementById(id);
+              if (note !== null) {
+                const html = processXRef(id, note);
+                instance.setContent(html);
+              } 
+            }).finally(() => {
+              instance.enable();
+              instance.show();
+            });
+          }
+        } else {
+          // See if we can fetch a full url (with no hash to target)
+          // This is a special case and we should probably do some content thinning / targeting
+          fetch(url)
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.querySelector('main.content');
+            if (note !== null) {
+              // This should only happen for chapter cross references
+              // (since there is no id in the URL)
+              // remove the first header
+              if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+                note.children[0].remove();
+              }
+              const html = processXRef(null, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      }, function(instance) {
+      });
+    }
+        let selectedAnnoteEl;
+        const selectorForAnnotation = ( cell, annotation) => {
+          let cellAttr = 'data-code-cell="' + cell + '"';
+          let lineAttr = 'data-code-annotation="' +  annotation + '"';
+          const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
+          return selector;
+        }
+        const selectCodeLines = (annoteEl) => {
+          const doc = window.document;
+          const targetCell = annoteEl.getAttribute("data-target-cell");
+          const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
+          const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
+          const lines = annoteSpan.getAttribute("data-code-lines").split(",");
+          const lineIds = lines.map((line) => {
+            return targetCell + "-" + line;
+          })
+          let top = null;
+          let height = null;
+          let parent = null;
+          if (lineIds.length > 0) {
+              //compute the position of the single el (top and bottom and make a div)
+              const el = window.document.getElementById(lineIds[0]);
+              top = el.offsetTop;
+              height = el.offsetHeight;
+              parent = el.parentElement.parentElement;
+            if (lineIds.length > 1) {
+              const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
+              const bottom = lastEl.offsetTop + lastEl.offsetHeight;
+              height = bottom - top;
+            }
+            if (top !== null && height !== null && parent !== null) {
+              // cook up a div (if necessary) and position it 
+              let div = window.document.getElementById("code-annotation-line-highlight");
+              if (div === null) {
+                div = window.document.createElement("div");
+                div.setAttribute("id", "code-annotation-line-highlight");
+                div.style.position = 'absolute';
+                parent.appendChild(div);
+              }
+              div.style.top = top - 2 + "px";
+              div.style.height = height + 4 + "px";
+              div.style.left = 0;
+              let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
+              if (gutterDiv === null) {
+                gutterDiv = window.document.createElement("div");
+                gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
+                gutterDiv.style.position = 'absolute';
+                const codeCell = window.document.getElementById(targetCell);
+                const gutter = codeCell.querySelector('.code-annotation-gutter');
+                gutter.appendChild(gutterDiv);
+              }
+              gutterDiv.style.top = top - 2 + "px";
+              gutterDiv.style.height = height + 4 + "px";
+            }
+            selectedAnnoteEl = annoteEl;
+          }
+        };
+        const unselectCodeLines = () => {
+          const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
+          elementsIds.forEach((elId) => {
+            const div = window.document.getElementById(elId);
+            if (div) {
+              div.remove();
+            }
+          });
+          selectedAnnoteEl = undefined;
+        };
+          // Handle positioning of the toggle
+      window.addEventListener(
+        "resize",
+        throttle(() => {
+          elRect = undefined;
+          if (selectedAnnoteEl) {
+            selectCodeLines(selectedAnnoteEl);
+          }
+        }, 10)
+      );
+      function throttle(fn, ms) {
+      let throttle = false;
+      let timer;
+        return (...args) => {
+          if(!throttle) { // first call gets through
+              fn.apply(this, args);
+              throttle = true;
+          } else { // all the others get throttled
+              if(timer) clearTimeout(timer); // cancel #2
+              timer = setTimeout(() => {
+                fn.apply(this, args);
+                timer = throttle = false;
+              }, ms);
+          }
+        };
+      }
+        // Attach click handler to the DT
+        const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
+        for (const annoteDlNode of annoteDls) {
+          annoteDlNode.addEventListener('click', (event) => {
+            const clickedEl = event.target;
+            if (clickedEl !== selectedAnnoteEl) {
+              unselectCodeLines();
+              const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
+              if (activeEl) {
+                activeEl.classList.remove('code-annotation-active');
+              }
+              selectCodeLines(clickedEl);
+              clickedEl.classList.add('code-annotation-active');
+            } else {
+              // Unselect the line
+              unselectCodeLines();
+              clickedEl.classList.remove('code-annotation-active');
+            }
+          });
+        }
+    const findCites = (el) => {
+      const parentEl = el.parentElement;
+      if (parentEl) {
+        const cites = parentEl.dataset.cites;
+        if (cites) {
+          return {
+            el,
+            cites: cites.split(' ')
+          };
+        } else {
+          return findCites(el.parentElement)
+        }
+      } else {
+        return undefined;
+      }
+    };
+    var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
+    for (var i=0; i<bibliorefs.length; i++) {
+      const ref = bibliorefs[i];
+      const citeInfo = findCites(ref);
+      if (citeInfo) {
+        tippyHover(citeInfo.el, function() {
+          var popup = window.document.createElement('div');
+          citeInfo.cites.forEach(function(cite) {
+            var citeDiv = window.document.createElement('div');
+            citeDiv.classList.add('hanging-indent');
+            citeDiv.classList.add('csl-entry');
+            var biblioDiv = window.document.getElementById('ref-' + cite);
+            if (biblioDiv) {
+              citeDiv.innerHTML = biblioDiv.innerHTML;
+            }
+            popup.appendChild(citeDiv);
+          });
+          return popup.innerHTML;
+        });
+      }
+    }
+  });
+  </script>
+</div> <!-- /content -->
+
+
+
+
+</body></html>
--- a/Readme.md
+++ b/Readme.md
@@ -1,146 +1,106 @@
-# JupyterHub Configuration with OrbStack on Mac (all in Docker)
+# OBIJupyterHub - the DNA Metabarcoding Learning Server

-## Prerequisites
+## Intended use

-You must have docker running on your computer
+This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and `./start-jupyterhub.sh` takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at `http://localhost:8888`. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.

-   On MacOS, [OrbStack](https://orbstack.dev/ "A Docker implementation optimised for MacOS") is recommanded
+## Prerequisites (with quick checks)

-## Installation Steps
+You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.

-### 1. Create Directory Structure
+- macOS: install [OrbStack](https://orbstack.dev/) (recommended) or Docker Desktop; both ship Docker Engine and Compose.
+- Linux: install Docker Engine and the Compose plugin from your distribution (e.g., `sudo apt install docker.io docker-compose-plugin`) or from Docker’s official packages.
+- Windows: install Docker Desktop with the WSL2 backend enabled.
+- Quarto CLI: get installers from <https://quarto.org/docs/get-started/>.
+- Python 3: any recent version is fine (only the standard library is used).
+
+Verify from a terminal; if a command is missing, install it before moving on:
+
+```bash
+docker --version
+docker compose version    # or: docker-compose --version
+quarto --version
+python3 --version
+```
+
+## How the startup script works
+
+`./start-jupyterhub.sh` is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:
+
+- creates the `jupyterhub_volumes/` tree (caddy, course, shared, users, web…)
+- builds `jupyterhub-student` and `jupyterhub-hub` images
+- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
+- runs `docker-compose up -d --remove-orphans`
+
+You can tailor what it does with a few flags:
+
+- `--no-build` (or `--offline`): skip Docker image builds and reuse existing images (useful when offline).
+- `--force-rebuild`: rebuild images without cache.
+- `--stop-server`: stop the stack and remove student containers, then exit.
+- `--update-lectures`: rebuild the course website only (no Docker stop/start).
+- `--build-obidoc`: force rebuilding the obidoc documentation (auto-built if empty; skipped in offline mode).
+
+## Installation and first run
+
+1) Clone the project:

 ```bash
 git clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git
-```
-
-Enter into the `OBIJupyterHub` directory
-
-```bash
 cd OBIJupyterHub
 ```

-#### File Structure
-
-Your `OBIJupyterHub` directory should contain:
+2) (Optional) glance at the structure you’ll populate:

 ```         
 OBIJupyterHub
-├── start-jupyterhub.sh                  - The script used to setup and start the server
-├── obijupyterhub                        - The files describing the docker images and the stack
-│   ├── Caddyfile
+├── start-jupyterhub.sh                  - single entry point (build + render + start)
+├── obijupyterhub                        - Docker images and stack definitions
 │   ├── docker-compose.yml
 │   ├── Dockerfile
 │   ├── Dockerfile.hub
-│   ├── jupyterhub_config.py
-│   ├── sftpgo_config.json
-│   └── start-notebook.sh
-├── jupyterhub_volumes                   - The directory containing the docker volumes
-│   ├── caddy
-│   ├── course                           - Read only volume mounted on every student container
-│   │   ├── bin
-│   │   └── R_packages
-│   ├── jupyterhub
-│   ├── shared                           - Read write volume shared in every student container
-│   ├── users
-│   └── web
-│       ├── img
-│       │   └── welcome_metabar.webp
-│       ├── index.html
-│       └── pages
-├── Readme.md                            - This documentation
-├── tools
-│   ├── generate_pages_json.py
-│   └── install_packages.sh
-└─── web_src                             - The quarto document sources used to build the web site
-    ├── _output
-    ├── _quarto.yml
-    ├── 00_home.qmd
-    ├── lectures
-    │   └── computers
-    │       └── regex
-    │           ├── lecture_regex.qmd
-    │           ├── slides_regex.qmd
-    │           └── slides.css
-    └── scripts
-         └── copy-to-web.sh
+│   └── jupyterhub_config.py
+├── jupyterhub_volumes                   - data persisted on the host
+│   ├── course                           - read-only for students (notebooks, data, bin, R packages)
+│   ├── shared                           - shared read/write space for everyone
+│   ├── users                            - per-user persistent data
+│   └── web                              - rendered course website
+└── web_src                              - Quarto sources for the course website
 ```

-### 2. Start JupyterHub
+3) Prepare course materials (optional before first run):
+- Put notebooks, datasets, scripts, binaries, or PDFs for students under `jupyterhub_volumes/course/`. They will appear read-only at `/home/jovyan/work/course/`.
+- For collaborative work, drop files in `jupyterhub_volumes/shared/` (read/write for all at `/home/jovyan/work/shared/`).
+- Edit or add Quarto sources in `web_src/` to update the course website; the script will render them.

-From the terminal, in the `OBIJupyterHub` directory, run the following command:
+4) Start everything (build + render + launch):

-``` bash
+```bash
 ./start-jupyterhub.sh
 ```

-### 3. Access JupyterHub
+5) Access JupyterHub in a browser at `http://localhost:8888`.

-Open your browser and go to: **http://localhost:8888**
+6) Stop the stack when you’re done (run from `obijupyterhub/`):

-You can log in as a student with any username and password: `metabar2025`
-
-## Useful Commands
-
-### View JupyterHub logs
-
-``` bash
-cd obijupyterhub
-docker-compose logs -f jupyterhub
-```
-
-### View all containers (hub + students)
-
-``` bash
-docker ps | grep jupyterhub
-```
-
-### Stop JupyterHub
-
-``` bash
-cd obijupyterhub
+```bash
 docker-compose down
 ```

-### Restart JupyterHub (after config modification)
+### Operating the stack (one command, a few options)

-``` bash
-cd obijupyterhub
-docker-compose restart jupyterhub
-```
+- Start or rebuild: `./start-jupyterhub.sh` (rebuilds images, regenerates the website, starts the stack).
+- Start without rebuilding images (offline): `./start-jupyterhub.sh --no-build`
+- Force rebuild without cache: `./start-jupyterhub.sh --force-rebuild`
+- Stop only: `./start-jupyterhub.sh --stop-server`
+- Rebuild website only (no Docker stop/start): `./start-jupyterhub.sh --update-lectures`
+- Rebuild obidoc docs: `./start-jupyterhub.sh --build-obidoc` (also builds automatically if `jupyterhub_volumes/web/obidoc` is empty; skipped in offline mode)
+- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
+- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
+- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.

-### View logs for a specific student
+## Managing shared data

-``` bash
-docker logs jupyter-<username>
-```
-
-Replace `<username>` by the actual username of the student.
-
-### Clean up after lab
-
-``` bash
-# Stop and remove all containers
-cd obijupyterhub
-docker-compose down
-
-# Remove student containers
-docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
-
-# Remove volumes (WARNING: deletes student data)
-docker volume ls | grep jupyterhub-user | awk '{print $2}' | xargs docker volume rm
-
-# Clean everything (containers + volumes + network)
-docker-compose down -v
-docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
-docker volume prune -f
-```
-
-## Managing Shared Data
-
-### Directory Structure for Each Student
-
-Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):
+Each student lands in `/home/jovyan/work/` with three key areas: their own files, a shared space, and a read-only course space. Everything under `work/` is persisted on the host in `jupyterhub_volumes`.

 ```         
 work/                             # Personal workspace root (persistent)
@@ -153,42 +113,22 @@ work/                             # Personal workspace root (persistent)
    └── [course materials]        # Your course files
 ```

-**R Package Priority:** 
-
-1. R checks `work/R_packages/` first (personal, writable) 
-1. Then `work/course/R_packages/` (shared, read-only, installed by prof) 
-1. Then system libraries
-
-**Important:** Everything is under `work/`, so all student files are automatically saved in their persistent volume.
+R looks for packages in this order: personal `work/R_packages/`, then shared `work/course/R_packages/`, then system libraries. Because everything lives under `work/`, student files survive restarts.

 ### User Accounts

-**Admin Account:** 
-
- Username: `admin` 
- Password: `admin2025` (change in docker-compose.yml: `JUPYTERHUB_ADMIN_PASSWORD`) 
- Can write to `course/` directory
-
-**Student Accounts:** 
-
- Username: any name 
- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`) 
- Read-only access to `course/` directory
+Defaults are defined in `obijupyterhub/docker-compose.yml`: admin (`admin` / `admin2025`) with write access to `course/`, and students (any username, password `metabar2025`) with read-only access to `course/`. Adjust `JUPYTERHUB_ADMIN_PASSWORD` and `JUPYTERHUB_PASSWORD` there, then rerun `./start-jupyterhub.sh`.

 ### Installing R Packages (Admin Only)

-**From your Mac (recommended):**
+From the host, install shared R packages into `course/R_packages/`:

 ``` bash
 # Install packages
 tools/install_packages.sh reshape2 plotly knitr
 ```

-This script: - Installs packages in the `course/R_packages/` directory - All students can use them (read-only) - No need to rebuild the image
-
-**Students can also install their own packages:**
-
-Students can install packages in their personal `work/R_packages/`:
+Students can install their own packages into their personal `work/R_packages/`:

 ```r
 # Install in personal library (each student has their own)
@@ -223,43 +163,9 @@ list.files("/home/jovyan/work/R_packages")
 list.files("/home/jovyan/work/course/R_packages")
 ```

-### Deposit Files for Course
+### Deposit or retrieve course and student files

-To put files in the `course/` directory (accessible read-only):
-
-``` bash
-# Create a temporary directory
-mkdir -p ~/jupyterhub-tp/course-files
-
-# Copy your files into it
-cp my_notebooks.ipynb ~/jupyterhub-tp/course-files/
-cp my_data.csv ~/jupyterhub-tp/course-files/
-
-# Copy into Docker volume
-docker run --rm \
-  -v jupyterhub-course:/target \
-  -v ~/jupyterhub-tp/course-files:/source \
-  alpine sh -c "cp -r /source/* /target/"
-```
-
-### Retrieve Student Work
-
-``` bash
-# List user volumes
-docker volume ls | grep 'obijupyterhub_user-'
-
-# Copy files from a specific student
-docker run --rm \
-  -v obijupyterhub_user-alice:/source \
-  -v ~/submissions:/target \
-  alpine sh -c "cp -r /source/* /target/alice/"
-
-# Copy all shared work
-docker run --rm \
-  -v obijupyterhub_shared:/source \
-  -v ~/submissions/shared:/target \
-  alpine sh -c "cp -r /source/* /target/"
-```
+On the host, place course files in `jupyterhub_volumes/course/` (they appear read-only to students), shared files in `jupyterhub_volumes/shared/`, and collect student work from `jupyterhub_volumes/users/`.

 ## User Management

@@ -299,11 +205,7 @@ Modify the `Dockerfile` (before `USER ${NB_UID}`):
 RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
 ```

-Then restart the server (it rebuilds the images if needed):
-
-```bash
-./start-jupyterhub.sh
-```
+Then rerun `./start-jupyterhub.sh` to rebuild and restart.

 ### Add Python Packages

@@ -313,14 +215,7 @@ Add to the `Dockerfile` (before `USER ${NB_UID}`):
 RUN pip install numpy pandas matplotlib seaborn
 ```

-### Distribute Files to Students
-
-Create a `files_lab/` directory and add to the `Dockerfile`:
-
-``` dockerfile
-COPY files_lab/ /home/${NB_USER}/lab/
-RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
-```
+Then rerun `./start-jupyterhub.sh` to rebuild and restart.

 ### Change Port (if 8000 is occupied)

@@ -341,29 +236,19 @@ ports:

 ## Troubleshooting

-**Error "Cannot connect to Docker daemon"**: 
-
- Check that OrbStack is running 
- Verify the socket exists: `ls -la /var/run/docker.sock`
-
-**Student containers don't start**: 
-
- Check logs: `docker-compose logs jupyterhub` 
- Verify student image exists: `docker images | grep jupyterhub-student`
-
-**Port 8000 already in use**: 
-
- Change port in `docker-compose.yml`
+- Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify `/var/run/docker.sock` exists.
+- Student containers do not start: check `docker-compose logs jupyterhub` and confirm the images exist with `docker images | grep jupyterhub-student`.
+- Port conflict: change the published port in `docker-compose.yml`.


 **I want to start from scratch**:

 ``` bash
-push obijupyterhub
+pushd obijupyterhub
 docker-compose down -v
 docker rmi jupyterhub-hub jupyterhub-student
 popd

 # Then rebuild everything
 ./start-jupyterhub.sh
-```
+```
--- a/Readme_files/libs/bootstrap/bootstrap-d6a003b94517c951b2d65075d42fb01b.min.css
+++ b/Readme_files/libs/bootstrap/bootstrap-d6a003b94517c951b2d65075d42fb01b.min.css
--- a/Readme_files/libs/bootstrap/bootstrap-icons.css
+++ b/Readme_files/libs/bootstrap/bootstrap-icons.css
--- a/Readme_files/libs/bootstrap/bootstrap-icons.woff
+++ b/Readme_files/libs/bootstrap/bootstrap-icons.woff
--- a/Readme_files/libs/bootstrap/bootstrap.min.js
+++ b/Readme_files/libs/bootstrap/bootstrap.min.js
--- a/Readme_files/libs/clipboard/clipboard.min.js
+++ b/Readme_files/libs/clipboard/clipboard.min.js
--- a/Readme_files/libs/quarto-html/anchor.min.js
+++ b/Readme_files/libs/quarto-html/anchor.min.js
--- a/Readme_files/libs/quarto-html/axe/axe-check.js
+++ b/Readme_files/libs/quarto-html/axe/axe-check.js
@@ -0,0 +1,145 @@
+class QuartoAxeReporter {
+  constructor(axeResult, options) {
+    this.axeResult = axeResult;
+    this.options = options;
+  }
+
+  report() {
+    throw new Error("report() is an abstract method");
+  }
+}
+
+class QuartoAxeJsonReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  report() {
+    console.log(JSON.stringify(this.axeResult, null, 2));
+  }
+}
+
+class QuartoAxeConsoleReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  report() {
+    for (const violation of this.axeResult.violations) {
+      console.log(violation.description);
+      for (const node of violation.nodes) {
+        for (const target of node.target) {
+          console.log(target);
+          console.log(document.querySelector(target));
+        }
+      }
+    }
+  }
+}
+
+class QuartoAxeDocumentReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  createViolationElement(violation) {
+    const violationElement = document.createElement("div");
+
+    const descriptionElement = document.createElement("div");
+    descriptionElement.className = "quarto-axe-violation-description";
+    descriptionElement.innerText = `${violation.impact.replace(/^[a-z]/, match => match.toLocaleUpperCase())}: ${violation.description}`;
+    violationElement.appendChild(descriptionElement);
+
+    const helpElement = document.createElement("div");
+    helpElement.className = "quarto-axe-violation-help";
+    helpElement.innerText = violation.help;
+    violationElement.appendChild(helpElement);
+
+    const nodesElement = document.createElement("div");
+    nodesElement.className = "quarto-axe-violation-nodes";
+    violationElement.appendChild(nodesElement);
+    const nodeElement = document.createElement("div");
+    nodeElement.className = "quarto-axe-violation-selector";
+    for (const node of violation.nodes) {
+      for (const target of node.target) {
+        const targetElement = document.createElement("span");
+        targetElement.className = "quarto-axe-violation-target";
+        targetElement.innerText = target;
+        nodeElement.appendChild(targetElement);
+        nodeElement.addEventListener("mouseenter", () => {
+          const element = document.querySelector(target);
+          if (element) {
+            element.scrollIntoView({ behavior: "smooth", block: "center" });
+            element.classList.add("quarto-axe-hover-highlight");
+            setTimeout(() => {
+              element.style.border = "";
+            }, 2000);
+          }
+        });
+        nodeElement.addEventListener("mouseleave", () => {
+          const element = document.querySelector(target);
+          if (element) {
+            element.classList.remove("quarto-axe-hover-highlight");
+          }
+        });
+        nodeElement.addEventListener("click", () => {
+          console.log(document.querySelector(target));
+        });
+        nodeElement.appendChild(targetElement);
+      }
+      nodesElement.appendChild(nodeElement);
+    }
+    return violationElement;
+  }
+
+  report() {
+    const violations = this.axeResult.violations;
+    const reportElement = document.createElement("div");
+    reportElement.className = "quarto-axe-report";
+    if (violations.length === 0) {
+      const noViolationsElement = document.createElement("div");
+      noViolationsElement.className = "quarto-axe-no-violations";
+      noViolationsElement.innerText = "No axe-core violations found.";
+      reportElement.appendChild(noViolationsElement);
+    }
+    violations.forEach((violation) => {
+      reportElement.appendChild(this.createViolationElement(violation));
+    });
+    document.querySelector("main").appendChild(reportElement);
+  }
+}
+
+const reporters = {
+  json: QuartoAxeJsonReporter,
+  console: QuartoAxeConsoleReporter,
+  document: QuartoAxeDocumentReporter,
+};
+
+class QuartoAxeChecker {
+  constructor(opts) {
+    this.options = opts;
+  }
+  async init() {
+    const axe = (await import("https://cdn.skypack.dev/pin/axe-core@v4.10.3-aVOFXWsJaCpVrtv89pCa/mode=imports,min/optimized/axe-core.js")).default;
+    const result = await axe.run({
+      exclude: [
+       // https://github.com/microsoft/tabster/issues/288
+       // MS has claimed they won't fix this, so we need to add an exclusion to
+       // all tabster elements
+       "[data-tabster-dummy]"
+      ],
+      preload: { assets: ['cssom'], timeout: 50000 }    
+    });
+    const reporter = this.options === true ? new QuartoAxeConsoleReporter(result) : new reporters[this.options.output](result, this.options);
+    reporter.report();
+  }
+}
+
+export async function init() {
+  const opts = document.querySelector("#quarto-axe-checker-options");
+  if (opts) {
+    const jsonOptions = JSON.parse(atob(opts.textContent));
+    const checker = new QuartoAxeChecker(jsonOptions);
+    await checker.init();
+  }
+}
--- a/Readme_files/libs/quarto-html/popper.min.js
+++ b/Readme_files/libs/quarto-html/popper.min.js
--- a/Readme_files/libs/quarto-html/quarto-syntax-highlighting-587c61ba64f3a5504c4d52d930310e48.css
+++ b/Readme_files/libs/quarto-html/quarto-syntax-highlighting-587c61ba64f3a5504c4d52d930310e48.css
@@ -0,0 +1,236 @@
+/* quarto syntax highlight colors */
+:root {
+  --quarto-hl-ot-color: #003B4F;
+  --quarto-hl-at-color: #657422;
+  --quarto-hl-ss-color: #20794D;
+  --quarto-hl-an-color: #5E5E5E;
+  --quarto-hl-fu-color: #4758AB;
+  --quarto-hl-st-color: #20794D;
+  --quarto-hl-cf-color: #003B4F;
+  --quarto-hl-op-color: #5E5E5E;
+  --quarto-hl-er-color: #AD0000;
+  --quarto-hl-bn-color: #AD0000;
+  --quarto-hl-al-color: #AD0000;
+  --quarto-hl-va-color: #111111;
+  --quarto-hl-bu-color: inherit;
+  --quarto-hl-ex-color: inherit;
+  --quarto-hl-pp-color: #AD0000;
+  --quarto-hl-in-color: #5E5E5E;
+  --quarto-hl-vs-color: #20794D;
+  --quarto-hl-wa-color: #5E5E5E;
+  --quarto-hl-do-color: #5E5E5E;
+  --quarto-hl-im-color: #00769E;
+  --quarto-hl-ch-color: #20794D;
+  --quarto-hl-dt-color: #AD0000;
+  --quarto-hl-fl-color: #AD0000;
+  --quarto-hl-co-color: #5E5E5E;
+  --quarto-hl-cv-color: #5E5E5E;
+  --quarto-hl-cn-color: #8f5902;
+  --quarto-hl-sc-color: #5E5E5E;
+  --quarto-hl-dv-color: #AD0000;
+  --quarto-hl-kw-color: #003B4F;
+}
+
+/* other quarto variables */
+:root {
+  --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
+}
+
+/* syntax highlight based on Pandoc's rules */
+pre > code.sourceCode > span {
+  color: #003B4F;
+}
+
+code.sourceCode > span {
+  color: #003B4F;
+}
+
+div.sourceCode,
+div.sourceCode pre.sourceCode {
+  color: #003B4F;
+}
+
+/* Normal */
+code span {
+  color: #003B4F;
+}
+
+/* Alert */
+code span.al {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* Annotation */
+code span.an {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+/* Attribute */
+code span.at {
+  color: #657422;
+  font-style: inherit;
+}
+
+/* BaseN */
+code span.bn {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* BuiltIn */
+code span.bu {
+  font-style: inherit;
+}
+
+/* ControlFlow */
+code span.cf {
+  color: #003B4F;
+  font-weight: bold;
+  font-style: inherit;
+}
+
+/* Char */
+code span.ch {
+  color: #20794D;
+  font-style: inherit;
+}
+
+/* Constant */
+code span.cn {
+  color: #8f5902;
+  font-style: inherit;
+}
+
+/* Comment */
+code span.co {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+/* CommentVar */
+code span.cv {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+/* Documentation */
+code span.do {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+/* DataType */
+code span.dt {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* DecVal */
+code span.dv {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* Error */
+code span.er {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* Extension */
+code span.ex {
+  font-style: inherit;
+}
+
+/* Float */
+code span.fl {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* Function */
+code span.fu {
+  color: #4758AB;
+  font-style: inherit;
+}
+
+/* Import */
+code span.im {
+  color: #00769E;
+  font-style: inherit;
+}
+
+/* Information */
+code span.in {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+/* Keyword */
+code span.kw {
+  color: #003B4F;
+  font-weight: bold;
+  font-style: inherit;
+}
+
+/* Operator */
+code span.op {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+/* Other */
+code span.ot {
+  color: #003B4F;
+  font-style: inherit;
+}
+
+/* Preprocessor */
+code span.pp {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+/* SpecialChar */
+code span.sc {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+/* SpecialString */
+code span.ss {
+  color: #20794D;
+  font-style: inherit;
+}
+
+/* String */
+code span.st {
+  color: #20794D;
+  font-style: inherit;
+}
+
+/* Variable */
+code span.va {
+  color: #111111;
+  font-style: inherit;
+}
+
+/* VerbatimString */
+code span.vs {
+  color: #20794D;
+  font-style: inherit;
+}
+
+/* Warning */
+code span.wa {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+.prevent-inlining {
+  content: "</";
+}
+
+/*# sourceMappingURL=2dce1cc6c82594539e1579de68416b47.css.map */
--- a/Readme_files/libs/quarto-html/quarto.js
+++ b/Readme_files/libs/quarto-html/quarto.js
@@ -0,0 +1,847 @@
+import * as tabsets from "./tabsets/tabsets.js";
+import * as axe from "./axe/axe-check.js";
+
+const sectionChanged = new CustomEvent("quarto-sectionChanged", {
+  detail: {},
+  bubbles: true,
+  cancelable: false,
+  composed: false,
+});
+
+const layoutMarginEls = () => {
+  // Find any conflicting margin elements and add margins to the
+  // top to prevent overlap
+  const marginChildren = window.document.querySelectorAll(
+    ".column-margin.column-container > *, .margin-caption, .aside"
+  );
+
+  let lastBottom = 0;
+  for (const marginChild of marginChildren) {
+    if (marginChild.offsetParent !== null) {
+      // clear the top margin so we recompute it
+      marginChild.style.marginTop = null;
+      const top = marginChild.getBoundingClientRect().top + window.scrollY;
+      if (top < lastBottom) {
+        const marginChildStyle = window.getComputedStyle(marginChild);
+        const marginBottom = parseFloat(marginChildStyle["marginBottom"]);
+        const margin = lastBottom - top + marginBottom;
+        marginChild.style.marginTop = `${margin}px`;
+      }
+      const styles = window.getComputedStyle(marginChild);
+      const marginTop = parseFloat(styles["marginTop"]);
+      lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
+    }
+  }
+};
+
+window.document.addEventListener("DOMContentLoaded", function (_event) {
+  // Recompute the position of margin elements anytime the body size changes
+  if (window.ResizeObserver) {
+    const resizeObserver = new window.ResizeObserver(
+      throttle(() => {
+        layoutMarginEls();
+        if (
+          window.document.body.getBoundingClientRect().width < 990 &&
+          isReaderMode()
+        ) {
+          quartoToggleReader();
+        }
+      }, 50)
+    );
+    resizeObserver.observe(window.document.body);
+  }
+
+  const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
+  const sidebarEl = window.document.getElementById("quarto-sidebar");
+  const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
+  const marginSidebarEl = window.document.getElementById(
+    "quarto-margin-sidebar"
+  );
+  // function to determine whether the element has a previous sibling that is active
+  const prevSiblingIsActiveLink = (el) => {
+    const sibling = el.previousElementSibling;
+    if (sibling && sibling.tagName === "A") {
+      return sibling.classList.contains("active");
+    } else {
+      return false;
+    }
+  };
+
+  // dispatch for htmlwidgets
+  // they use slideenter event to trigger resize
+  function fireSlideEnter() {
+    const event = window.document.createEvent("Event");
+    event.initEvent("slideenter", true, true);
+    window.document.dispatchEvent(event);
+  }
+
+  const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
+  tabs.forEach((tab) => {
+    tab.addEventListener("shown.bs.tab", fireSlideEnter);
+  });
+
+  // dispatch for shiny
+  // they use BS shown and hidden events to trigger rendering
+  function distpatchShinyEvents(previous, current) {
+    if (window.jQuery) {
+      if (previous) {
+        window.jQuery(previous).trigger("hidden");
+      }
+      if (current) {
+        window.jQuery(current).trigger("shown");
+      }
+    }
+  }
+
+  // tabby.js listener: Trigger event for htmlwidget and shiny
+  document.addEventListener(
+    "tabby",
+    function (event) {
+      fireSlideEnter();
+      distpatchShinyEvents(event.detail.previousTab, event.detail.tab);
+    },
+    false
+  );
+
+  // Track scrolling and mark TOC links as active
+  // get table of contents and sidebar (bail if we don't have at least one)
+  const tocLinks = tocEl
+    ? [...tocEl.querySelectorAll("a[data-scroll-target]")]
+    : [];
+  const makeActive = (link) => tocLinks[link].classList.add("active");
+  const removeActive = (link) => tocLinks[link].classList.remove("active");
+  const removeAllActive = () =>
+    [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
+
+  // activate the anchor for a section associated with this TOC entry
+  tocLinks.forEach((link) => {
+    link.addEventListener("click", () => {
+      if (link.href.indexOf("#") !== -1) {
+        const anchor = link.href.split("#")[1];
+        const heading = window.document.querySelector(
+          `[data-anchor-id="${anchor}"]`
+        );
+        if (heading) {
+          // Add the class
+          heading.classList.add("reveal-anchorjs-link");
+
+          // function to show the anchor
+          const handleMouseout = () => {
+            heading.classList.remove("reveal-anchorjs-link");
+            heading.removeEventListener("mouseout", handleMouseout);
+          };
+
+          // add a function to clear the anchor when the user mouses out of it
+          heading.addEventListener("mouseout", handleMouseout);
+        }
+      }
+    });
+  });
+
+  const sections = tocLinks.map((link) => {
+    const target = link.getAttribute("data-scroll-target");
+    if (target.startsWith("#")) {
+      return window.document.getElementById(decodeURI(`${target.slice(1)}`));
+    } else {
+      return window.document.querySelector(decodeURI(`${target}`));
+    }
+  });
+
+  const sectionMargin = 200;
+  let currentActive = 0;
+  // track whether we've initialized state the first time
+  let init = false;
+
+  const updateActiveLink = () => {
+    // The index from bottom to top (e.g. reversed list)
+    let sectionIndex = -1;
+    if (
+      window.innerHeight + window.pageYOffset >=
+      window.document.body.offsetHeight
+    ) {
+      // This is the no-scroll case where last section should be the active one
+      sectionIndex = 0;
+    } else {
+      // This finds the last section visible on screen that should be made active
+      sectionIndex = [...sections].reverse().findIndex((section) => {
+        if (section) {
+          return window.pageYOffset >= section.offsetTop - sectionMargin;
+        } else {
+          return false;
+        }
+      });
+    }
+    if (sectionIndex > -1) {
+      const current = sections.length - sectionIndex - 1;
+      if (current !== currentActive) {
+        removeAllActive();
+        currentActive = current;
+        makeActive(current);
+        if (init) {
+          window.dispatchEvent(sectionChanged);
+        }
+        init = true;
+      }
+    }
+  };
+
+  const inHiddenRegion = (top, bottom, hiddenRegions) => {
+    for (const region of hiddenRegions) {
+      if (top <= region.bottom && bottom >= region.top) {
+        return true;
+      }
+    }
+    return false;
+  };
+
+  const categorySelector = "header.quarto-title-block .quarto-category";
+  const activateCategories = (href) => {
+    // Find any categories
+    // Surround them with a link pointing back to:
+    // #category=Authoring
+    try {
+      const categoryEls = window.document.querySelectorAll(categorySelector);
+      for (const categoryEl of categoryEls) {
+        const categoryText = categoryEl.textContent;
+        if (categoryText) {
+          const link = `${href}#category=${encodeURIComponent(categoryText)}`;
+          const linkEl = window.document.createElement("a");
+          linkEl.setAttribute("href", link);
+          for (const child of categoryEl.childNodes) {
+            linkEl.append(child);
+          }
+          categoryEl.appendChild(linkEl);
+        }
+      }
+    } catch {
+      // Ignore errors
+    }
+  };
+  function hasTitleCategories() {
+    return window.document.querySelector(categorySelector) !== null;
+  }
+
+  function offsetRelativeUrl(url) {
+    const offset = getMeta("quarto:offset");
+    return offset ? offset + url : url;
+  }
+
+  function offsetAbsoluteUrl(url) {
+    const offset = getMeta("quarto:offset");
+    const baseUrl = new URL(offset, window.location);
+
+    const projRelativeUrl = url.replace(baseUrl, "");
+    if (projRelativeUrl.startsWith("/")) {
+      return projRelativeUrl;
+    } else {
+      return "/" + projRelativeUrl;
+    }
+  }
+
+  // read a meta tag value
+  function getMeta(metaName) {
+    const metas = window.document.getElementsByTagName("meta");
+    for (let i = 0; i < metas.length; i++) {
+      if (metas[i].getAttribute("name") === metaName) {
+        return metas[i].getAttribute("content");
+      }
+    }
+    return "";
+  }
+
+  async function findAndActivateCategories() {
+    // Categories search with listing only use path without query
+    const currentPagePath = offsetAbsoluteUrl(
+      window.location.origin + window.location.pathname
+    );
+    const response = await fetch(offsetRelativeUrl("listings.json"));
+    if (response.status == 200) {
+      return response.json().then(function (listingPaths) {
+        const listingHrefs = [];
+        for (const listingPath of listingPaths) {
+          const pathWithoutLeadingSlash = listingPath.listing.substring(1);
+          for (const item of listingPath.items) {
+            const encodedItem = encodeURI(item);
+            if (
+              encodedItem === currentPagePath ||
+              encodedItem === currentPagePath + "index.html"
+            ) {
+              // Resolve this path against the offset to be sure
+              // we already are using the correct path to the listing
+              // (this adjusts the listing urls to be rooted against
+              // whatever root the page is actually running against)
+              const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
+              const baseUrl = window.location;
+              const resolvedPath = new URL(relative, baseUrl);
+              listingHrefs.push(resolvedPath.pathname);
+              break;
+            }
+          }
+        }
+
+        // Look up the tree for a nearby linting and use that if we find one
+        const nearestListing = findNearestParentListing(
+          offsetAbsoluteUrl(window.location.pathname),
+          listingHrefs
+        );
+        if (nearestListing) {
+          activateCategories(nearestListing);
+        } else {
+          // See if the referrer is a listing page for this item
+          const referredRelativePath = offsetAbsoluteUrl(document.referrer);
+          const referrerListing = listingHrefs.find((listingHref) => {
+            const isListingReferrer =
+              listingHref === referredRelativePath ||
+              listingHref === referredRelativePath + "index.html";
+            return isListingReferrer;
+          });
+
+          if (referrerListing) {
+            // Try to use the referrer if possible
+            activateCategories(referrerListing);
+          } else if (listingHrefs.length > 0) {
+            // Otherwise, just fall back to the first listing
+            activateCategories(listingHrefs[0]);
+          }
+        }
+      });
+    }
+  }
+  if (hasTitleCategories()) {
+    findAndActivateCategories();
+  }
+
+  const findNearestParentListing = (href, listingHrefs) => {
+    if (!href || !listingHrefs) {
+      return undefined;
+    }
+    // Look up the tree for a nearby linting and use that if we find one
+    const relativeParts = href.substring(1).split("/");
+    while (relativeParts.length > 0) {
+      const path = relativeParts.join("/");
+      for (const listingHref of listingHrefs) {
+        if (listingHref.startsWith(path)) {
+          return listingHref;
+        }
+      }
+      relativeParts.pop();
+    }
+
+    return undefined;
+  };
+
+  const manageSidebarVisiblity = (el, placeholderDescriptor) => {
+    let isVisible = true;
+    let elRect;
+
+    return (hiddenRegions) => {
+      if (el === null) {
+        return;
+      }
+
+      // Find the last element of the TOC
+      const lastChildEl = el.lastElementChild;
+
+      if (lastChildEl) {
+        // Converts the sidebar to a menu
+        const convertToMenu = () => {
+          for (const child of el.children) {
+            child.style.opacity = 0;
+            child.style.overflow = "hidden";
+            child.style.pointerEvents = "none";
+          }
+
+          nexttick(() => {
+            const toggleContainer = window.document.createElement("div");
+            toggleContainer.style.width = "100%";
+            toggleContainer.classList.add("zindex-over-content");
+            toggleContainer.classList.add("quarto-sidebar-toggle");
+            toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
+            toggleContainer.id = placeholderDescriptor.id;
+            toggleContainer.style.position = "fixed";
+
+            const toggleIcon = window.document.createElement("i");
+            toggleIcon.classList.add("quarto-sidebar-toggle-icon");
+            toggleIcon.classList.add("bi");
+            toggleIcon.classList.add("bi-caret-down-fill");
+
+            const toggleTitle = window.document.createElement("div");
+            const titleEl = window.document.body.querySelector(
+              placeholderDescriptor.titleSelector
+            );
+            if (titleEl) {
+              toggleTitle.append(
+                titleEl.textContent || titleEl.innerText,
+                toggleIcon
+              );
+            }
+            toggleTitle.classList.add("zindex-over-content");
+            toggleTitle.classList.add("quarto-sidebar-toggle-title");
+            toggleContainer.append(toggleTitle);
+
+            const toggleContents = window.document.createElement("div");
+            toggleContents.classList = el.classList;
+            toggleContents.classList.add("zindex-over-content");
+            toggleContents.classList.add("quarto-sidebar-toggle-contents");
+            for (const child of el.children) {
+              if (child.id === "toc-title") {
+                continue;
+              }
+
+              const clone = child.cloneNode(true);
+              clone.style.opacity = 1;
+              clone.style.pointerEvents = null;
+              clone.style.display = null;
+              toggleContents.append(clone);
+            }
+            toggleContents.style.height = "0px";
+            const positionToggle = () => {
+              // position the element (top left of parent, same width as parent)
+              if (!elRect) {
+                elRect = el.getBoundingClientRect();
+              }
+              toggleContainer.style.left = `${elRect.left}px`;
+              toggleContainer.style.top = `${elRect.top}px`;
+              toggleContainer.style.width = `${elRect.width}px`;
+            };
+            positionToggle();
+
+            toggleContainer.append(toggleContents);
+            el.parentElement.prepend(toggleContainer);
+
+            // Process clicks
+            let tocShowing = false;
+            // Allow the caller to control whether this is dismissed
+            // when it is clicked (e.g. sidebar navigation supports
+            // opening and closing the nav tree, so don't dismiss on click)
+            const clickEl = placeholderDescriptor.dismissOnClick
+              ? toggleContainer
+              : toggleTitle;
+
+            const closeToggle = () => {
+              if (tocShowing) {
+                toggleContainer.classList.remove("expanded");
+                toggleContents.style.height = "0px";
+                tocShowing = false;
+              }
+            };
+
+            // Get rid of any expanded toggle if the user scrolls
+            window.document.addEventListener(
+              "scroll",
+              throttle(() => {
+                closeToggle();
+              }, 50)
+            );
+
+            // Handle positioning of the toggle
+            window.addEventListener(
+              "resize",
+              throttle(() => {
+                elRect = undefined;
+                positionToggle();
+              }, 50)
+            );
+
+            window.addEventListener("quarto-hrChanged", () => {
+              elRect = undefined;
+            });
+
+            // Process the click
+            clickEl.onclick = () => {
+              if (!tocShowing) {
+                toggleContainer.classList.add("expanded");
+                toggleContents.style.height = null;
+                tocShowing = true;
+              } else {
+                closeToggle();
+              }
+            };
+          });
+        };
+
+        // Converts a sidebar from a menu back to a sidebar
+        const convertToSidebar = () => {
+          for (const child of el.children) {
+            child.style.opacity = 1;
+            child.style.overflow = null;
+            child.style.pointerEvents = null;
+          }
+
+          const placeholderEl = window.document.getElementById(
+            placeholderDescriptor.id
+          );
+          if (placeholderEl) {
+            placeholderEl.remove();
+          }
+
+          el.classList.remove("rollup");
+        };
+
+        if (isReaderMode()) {
+          convertToMenu();
+          isVisible = false;
+        } else {
+          // Find the top and bottom o the element that is being managed
+          const elTop = el.offsetTop;
+          const elBottom =
+            elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
+
+          if (!isVisible) {
+            // If the element is current not visible reveal if there are
+            // no conflicts with overlay regions
+            if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToSidebar();
+              isVisible = true;
+            }
+          } else {
+            // If the element is visible, hide it if it conflicts with overlay regions
+            // and insert a placeholder toggle (or if we're in reader mode)
+            if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToMenu();
+              isVisible = false;
+            }
+          }
+        }
+      }
+    };
+  };
+
+  const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
+  for (const tabEl of tabEls) {
+    const id = tabEl.getAttribute("data-bs-target");
+    if (id) {
+      const columnEl = document.querySelector(
+        `${id} .column-margin, .tabset-margin-content`
+      );
+      if (columnEl)
+        tabEl.addEventListener("shown.bs.tab", function (event) {
+          const el = event.srcElement;
+          if (el) {
+            const visibleCls = `${el.id}-margin-content`;
+            // walk up until we find a parent tabset
+            let panelTabsetEl = el.parentElement;
+            while (panelTabsetEl) {
+              if (panelTabsetEl.classList.contains("panel-tabset")) {
+                break;
+              }
+              panelTabsetEl = panelTabsetEl.parentElement;
+            }
+
+            if (panelTabsetEl) {
+              const prevSib = panelTabsetEl.previousElementSibling;
+              if (
+                prevSib &&
+                prevSib.classList.contains("tabset-margin-container")
+              ) {
+                const childNodes = prevSib.querySelectorAll(
+                  ".tabset-margin-content"
+                );
+                for (const childEl of childNodes) {
+                  if (childEl.classList.contains(visibleCls)) {
+                    childEl.classList.remove("collapse");
+                  } else {
+                    childEl.classList.add("collapse");
+                  }
+                }
+              }
+            }
+          }
+
+          layoutMarginEls();
+        });
+    }
+  }
+
+  // Manage the visibility of the toc and the sidebar
+  const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
+    id: "quarto-toc-toggle",
+    titleSelector: "#toc-title",
+    dismissOnClick: true,
+  });
+  const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
+    id: "quarto-sidebarnav-toggle",
+    titleSelector: ".title",
+    dismissOnClick: false,
+  });
+  let tocLeftScrollVisibility;
+  if (leftTocEl) {
+    tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
+      id: "quarto-lefttoc-toggle",
+      titleSelector: "#toc-title",
+      dismissOnClick: true,
+    });
+  }
+
+  // Find the first element that uses formatting in special columns
+  const conflictingEls = window.document.body.querySelectorAll(
+    '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
+  );
+
+  // Filter all the possibly conflicting elements into ones
+  // the do conflict on the left or ride side
+  const arrConflictingEls = Array.from(conflictingEls);
+  const leftSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return false;
+    }
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        className.startsWith("column-") &&
+        !className.endsWith("right") &&
+        !className.endsWith("container") &&
+        className !== "column-margin"
+      );
+    });
+  });
+  const rightSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return true;
+    }
+
+    const hasMarginCaption = Array.from(el.classList).find((className) => {
+      return className == "margin-caption";
+    });
+    if (hasMarginCaption) {
+      return true;
+    }
+
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        !className.endsWith("container") &&
+        className.startsWith("column-") &&
+        !className.endsWith("left")
+      );
+    });
+  });
+
+  const kOverlapPaddingSize = 10;
+  function toRegions(els) {
+    return els.map((el) => {
+      const boundRect = el.getBoundingClientRect();
+      const top =
+        boundRect.top +
+        document.documentElement.scrollTop -
+        kOverlapPaddingSize;
+      return {
+        top,
+        bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
+      };
+    });
+  }
+
+  let hasObserved = false;
+  const visibleItemObserver = (els) => {
+    let visibleElements = [...els];
+    const intersectionObserver = new IntersectionObserver(
+      (entries, _observer) => {
+        entries.forEach((entry) => {
+          if (entry.isIntersecting) {
+            if (visibleElements.indexOf(entry.target) === -1) {
+              visibleElements.push(entry.target);
+            }
+          } else {
+            visibleElements = visibleElements.filter((visibleEntry) => {
+              return visibleEntry !== entry;
+            });
+          }
+        });
+
+        if (!hasObserved) {
+          hideOverlappedSidebars();
+        }
+        hasObserved = true;
+      },
+      {}
+    );
+    els.forEach((el) => {
+      intersectionObserver.observe(el);
+    });
+
+    return {
+      getVisibleEntries: () => {
+        return visibleElements;
+      },
+    };
+  };
+
+  const rightElementObserver = visibleItemObserver(rightSideConflictEls);
+  const leftElementObserver = visibleItemObserver(leftSideConflictEls);
+
+  const hideOverlappedSidebars = () => {
+    marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
+    sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
+    if (tocLeftScrollVisibility) {
+      tocLeftScrollVisibility(
+        toRegions(leftElementObserver.getVisibleEntries())
+      );
+    }
+  };
+
+  window.quartoToggleReader = () => {
+    // Applies a slow class (or removes it)
+    // to update the transition speed
+    const slowTransition = (slow) => {
+      const manageTransition = (id, slow) => {
+        const el = document.getElementById(id);
+        if (el) {
+          if (slow) {
+            el.classList.add("slow");
+          } else {
+            el.classList.remove("slow");
+          }
+        }
+      };
+
+      manageTransition("TOC", slow);
+      manageTransition("quarto-sidebar", slow);
+    };
+    const readerMode = !isReaderMode();
+    setReaderModeValue(readerMode);
+
+    // If we're entering reader mode, slow the transition
+    if (readerMode) {
+      slowTransition(readerMode);
+    }
+    highlightReaderToggle(readerMode);
+    hideOverlappedSidebars();
+
+    // If we're exiting reader mode, restore the non-slow transition
+    if (!readerMode) {
+      slowTransition(!readerMode);
+    }
+  };
+
+  const highlightReaderToggle = (readerMode) => {
+    const els = document.querySelectorAll(".quarto-reader-toggle");
+    if (els) {
+      els.forEach((el) => {
+        if (readerMode) {
+          el.classList.add("reader");
+        } else {
+          el.classList.remove("reader");
+        }
+      });
+    }
+  };
+
+  const setReaderModeValue = (val) => {
+    if (window.location.protocol !== "file:") {
+      window.localStorage.setItem("quarto-reader-mode", val);
+    } else {
+      localReaderMode = val;
+    }
+  };
+
+  const isReaderMode = () => {
+    if (window.location.protocol !== "file:") {
+      return window.localStorage.getItem("quarto-reader-mode") === "true";
+    } else {
+      return localReaderMode;
+    }
+  };
+  let localReaderMode = null;
+
+  const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
+  const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
+
+  // Walk the TOC and collapse/expand nodes
+  // Nodes are expanded if:
+  // - they are top level
+  // - they have children that are 'active' links
+  // - they are directly below an link that is 'active'
+  const walk = (el, depth) => {
+    // Tick depth when we enter a UL
+    if (el.tagName === "UL") {
+      depth = depth + 1;
+    }
+
+    // It this is active link
+    let isActiveNode = false;
+    if (el.tagName === "A" && el.classList.contains("active")) {
+      isActiveNode = true;
+    }
+
+    // See if there is an active child to this element
+    let hasActiveChild = false;
+    for (const child of el.children) {
+      hasActiveChild = walk(child, depth) || hasActiveChild;
+    }
+
+    // Process the collapse state if this is an UL
+    if (el.tagName === "UL") {
+      if (tocOpenDepth === -1 && depth > 1) {
+        // toc-expand: false
+        el.classList.add("collapse");
+      } else if (
+        depth <= tocOpenDepth ||
+        hasActiveChild ||
+        prevSiblingIsActiveLink(el)
+      ) {
+        el.classList.remove("collapse");
+      } else {
+        el.classList.add("collapse");
+      }
+
+      // untick depth when we leave a UL
+      depth = depth - 1;
+    }
+    return hasActiveChild || isActiveNode;
+  };
+
+  // walk the TOC and expand / collapse any items that should be shown
+  if (tocEl) {
+    updateActiveLink();
+    walk(tocEl, 0);
+  }
+
+  // Throttle the scroll event and walk peridiocally
+  window.document.addEventListener(
+    "scroll",
+    throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 5)
+  );
+  window.addEventListener(
+    "resize",
+    throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 10)
+  );
+  hideOverlappedSidebars();
+  highlightReaderToggle(isReaderMode());
+});
+
+tabsets.init();
+axe.init();
+
+function throttle(func, wait) {
+  let waiting = false;
+  return function () {
+    if (!waiting) {
+      func.apply(this, arguments);
+      waiting = true;
+      setTimeout(function () {
+        waiting = false;
+      }, wait);
+    }
+  };
+}
+
+function nexttick(func) {
+  return setTimeout(func, 0);
+}
--- a/Readme_files/libs/quarto-html/tabsets/tabsets.js
+++ b/Readme_files/libs/quarto-html/tabsets/tabsets.js
@@ -0,0 +1,95 @@
+// grouped tabsets
+
+export function init() {
+  window.addEventListener("pageshow", (_event) => {
+    function getTabSettings() {
+      const data = localStorage.getItem("quarto-persistent-tabsets-data");
+      if (!data) {
+        localStorage.setItem("quarto-persistent-tabsets-data", "{}");
+        return {};
+      }
+      if (data) {
+        return JSON.parse(data);
+      }
+    }
+
+    function setTabSettings(data) {
+      localStorage.setItem(
+        "quarto-persistent-tabsets-data",
+        JSON.stringify(data)
+      );
+    }
+
+    function setTabState(groupName, groupValue) {
+      const data = getTabSettings();
+      data[groupName] = groupValue;
+      setTabSettings(data);
+    }
+
+    function toggleTab(tab, active) {
+      const tabPanelId = tab.getAttribute("aria-controls");
+      const tabPanel = document.getElementById(tabPanelId);
+      if (active) {
+        tab.classList.add("active");
+        tabPanel.classList.add("active");
+      } else {
+        tab.classList.remove("active");
+        tabPanel.classList.remove("active");
+      }
+    }
+
+    function toggleAll(selectedGroup, selectorsToSync) {
+      for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
+        const active = selectedGroup === thisGroup;
+        for (const tab of tabs) {
+          toggleTab(tab, active);
+        }
+      }
+    }
+
+    function findSelectorsToSyncByLanguage() {
+      const result = {};
+      const tabs = Array.from(
+        document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
+      );
+      for (const item of tabs) {
+        const div = item.parentElement.parentElement.parentElement;
+        const group = div.getAttribute("data-group");
+        if (!result[group]) {
+          result[group] = {};
+        }
+        const selectorsToSync = result[group];
+        const value = item.innerHTML;
+        if (!selectorsToSync[value]) {
+          selectorsToSync[value] = [];
+        }
+        selectorsToSync[value].push(item);
+      }
+      return result;
+    }
+
+    function setupSelectorSync() {
+      const selectorsToSync = findSelectorsToSyncByLanguage();
+      Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
+        Object.entries(tabSetsByValue).forEach(([value, items]) => {
+          items.forEach((item) => {
+            item.addEventListener("click", (_event) => {
+              setTabState(group, value);
+              toggleAll(value, selectorsToSync[group]);
+            });
+          });
+        });
+      });
+      return selectorsToSync;
+    }
+
+    const selectorsToSync = setupSelectorSync();
+    for (const [group, selectedName] of Object.entries(getTabSettings())) {
+      const selectors = selectorsToSync[group];
+      // it's possible that stale state gives us empty selections, so we explicitly check here.
+      if (selectors) {
+        toggleAll(selectedName, selectors);
+      }
+    }
+  });
+}
--- a/Readme_files/libs/quarto-html/tippy.css
+++ b/Readme_files/libs/quarto-html/tippy.css
@@ -0,0 +1 @@
+.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
--- a/Readme_files/libs/quarto-html/tippy.umd.min.js
+++ b/Readme_files/libs/quarto-html/tippy.umd.min.js
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf_F.fastq
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_F.fastq
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf_R.fastq
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_R.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_diet_ngsfilter.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_diet_ngsfilter.csv
--- a/jupyterhub_volumes/web/.gitignore
+++ b/jupyterhub_volumes/web/.gitignore
@@ -1,3 +1,4 @@
 /.quarto/
 **/*.quarto_ipynb
-/pages/
+/pages/
+/obidoc/
--- a/jupyterhub_volumes/web/obidoc/404.html
+++ b/jupyterhub_volumes/web/obidoc/404.html
@@ -1,56 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-
-  <head>
-    <meta charset="UTF-8">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="description" content="">
-<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
-<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
-<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/404.html">
-  <meta property="og:site_name" content="OBITools4 documentation">
-  <meta property="og:title" content="404 Page not found">
-  <meta property="og:locale" content="en_us">
-  <meta property="og:type" content="website">
-<title>404 Page not found | OBITools4 documentation</title>
-<link rel="icon" href="/obidoc/favicon.png" >
-<link rel="manifest" href="/obidoc/manifest.json">
-<link rel="canonical" href="http://metabar:8888/obidoc/404.html">
-<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb&#43;a3g=" crossorigin="anonymous">
-  <script defer src="/obidoc/fuse.min.js"></script>
-  <script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
-
-  <script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq&#43;Or85BgKocXepm2Z&#43;ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
-<!--
-Made with Book Theme
-https://github.com/alex-shpak/hugo-book
-->
-    <link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
-
-    <style>
-      .not-found {
-        text-align: center;
-      }
-      .not-found h1 {
-        margin: .25em 0 0 0;
-        opacity: .25;
-        font-size: 40vmin;
-      }
-    </style>
-  </head>
-
-  <body>
-    <main class="flex justify-center not-found">
-      <div>
-        <h1>404</h1>
-        <h2>Page Not Found</h2>
-        <h3>
-          <a href="/obidoc/">OBITools4 documentation</a>
-        </h3>
-      </div>
-    </main>
-
-    
-  </body>
-
-  </html>
--- a/jupyterhub_volumes/web/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css
+++ b/jupyterhub_volumes/web/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css
--- a/jupyterhub_volumes/web/obidoc/categories/index.html
+++ b/jupyterhub_volumes/web/obidoc/categories/index.html
--- a/jupyterhub_volumes/web/obidoc/categories/index.xml
+++ b/jupyterhub_volumes/web/obidoc/categories/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Categories on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/categories/</link>
-    <description>Recent content in Categories on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/categories/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/categories/page/1/index.html
+++ b/jupyterhub_volumes/web/obidoc/categories/page/1/index.html
@@ -1,9 +0,0 @@
-<!DOCTYPE html>
-<html lang="en-us">
-  <head>
-    <title>http://metabar:8888/obidoc/categories/</title>
-    <link rel="canonical" href="http://metabar:8888/obidoc/categories/">
-    <meta charset="utf-8">
-    <meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/categories/">
-  </head>
-</html>
--- a/jupyterhub_volumes/web/obidoc/commands/index.html
+++ b/jupyterhub_volumes/web/obidoc/commands/index.html
--- a/jupyterhub_volumes/web/obidoc/commands/index.xml
+++ b/jupyterhub_volumes/web/obidoc/commands/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Commands on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/commands/</link>
-    <description>Recent content in Commands on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/commands/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/commands/page/1/index.html
+++ b/jupyterhub_volumes/web/obidoc/commands/page/1/index.html
@@ -1,9 +0,0 @@
-<!DOCTYPE html>
-<html lang="en-us">
-  <head>
-    <title>http://metabar:8888/obidoc/commands/</title>
-    <link rel="canonical" href="http://metabar:8888/obidoc/commands/">
-    <meta charset="utf-8">
-    <meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/commands/">
-  </head>
-</html>
--- a/jupyterhub_volumes/web/obidoc/css/vendors/admonitions.5c73bad2903e7d2d44ad118370ebd8c2cf5f239d4d93c283e55c00f2f8d30746.css
+++ b/jupyterhub_volumes/web/obidoc/css/vendors/admonitions.5c73bad2903e7d2d44ad118370ebd8c2cf5f239d4d93c283e55c00f2f8d30746.css
@@ -1 +0,0 @@
-.admonition{margin:1rem 0;border-radius:4px;box-shadow:0 1px 3px rgba(0,0,0,0.12);transition:all 0.3s ease}.admonition-header{padding:0.5rem 1rem;display:flex;align-items:center;font-weight:600;border-bottom:1px solid rgba(0,0,0,0.1);font-size:1.1rem;border-radius:4px 4px 0 0}.admonition-header svg{width:1.1em;height:1.1em;margin-right:0.5rem;fill:currentColor}.admonition-content{padding:1rem;background-color:#fff;border-radius:0 0 4px 4px;color:#000;transition:background-color 0.3s ease, color 0.3s ease}.admonition-content p{margin:0 0 0.5rem 0}.admonition-content p:last-child{margin-bottom:0}.admonition-content ul,.admonition-content ol{margin:0 0 0.5rem 0;padding-left:1.2rem}.admonition-content ul:last-child,.admonition-content ol:last-child{margin-bottom:0}.admonition-content blockquote{margin:0 0 0.5rem 0;padding-left:1rem;border-left:3px solid #e0e0e0}.admonition-content blockquote:last-child{margin-bottom:0}.admonition-content code{background-color:#f5f5f5;color:#24292e;padding:0.2em 0.4em;border-radius:3px;font-size:0.9em}@media (prefers-color-scheme: dark){.admonition-content{background-color:#1D1E20;color:#e6e6e6}.admonition-content code{background-color:#313244;color:#cdd6f4}.admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}}body.dark .admonition-content{background-color:#1D1E20;color:#e6e6e6}body.dark .admonition-content code{background-color:#313244;color:#cdd6f4}body.dark .admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}.admonition.abstract{background:transparent;border-left:4px solid #209fb5}.admonition.abstract .admonition-header{background:rgba(32,159,181,0.1);color:#209fb5}.admonition.caution{background:transparent;border-left:4px solid #e64553}.admonition.caution .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.code{background:transparent;border-left:4px solid #7287fd}.admonition.code .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.conclusion{background:transparent;border-left:4px solid #dd7878}.admonition.conclusion .admonition-header{background:rgba(221,120,120,0.1);color:#dd7878}.admonition.danger{background:transparent;border-left:4px solid #fe640b}.admonition.danger .admonition-header{background:rgba(254,100,11,0.1);color:#fe640b}.admonition.error{background:transparent;border-left:4px solid #d20f39}.admonition.error .admonition-header{background:rgba(210,15,57,0.1);color:#d20f39}.admonition.example{background:transparent;border-left:4px solid #dc8a78}.admonition.example .admonition-header{background:rgba(220,138,120,0.1);color:#dc8a78}.admonition.experiment{background:transparent;border-left:4px solid #51bb2a}.admonition.experiment .admonition-header{background:rgba(81,187,42,0.1);color:#51bb2a}.admonition.goal{background:transparent;border-left:4px solid #e64553}.admonition.goal .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.idea{background:transparent;border-left:4px solid #df8e1d}.admonition.idea .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}.admonition.important{background:transparent;border-left:4px solid #7D4DDA}.admonition.important .admonition-header{background:rgba(125,77,218,0.1);color:#7D4DDA}.admonition.info{background:transparent;border-left:4px solid #04a5e5}.admonition.info .admonition-header{background:rgba(4,165,229,0.1);color:#04a5e5}.admonition.memo{background:transparent;border-left:4px solid #e64553}.admonition.memo .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.note{background:transparent;border-left:4px solid #096ae1}.admonition.note .admonition-header{background:rgba(9,106,225,0.1);color:#096ae1}.admonition.notify{background:transparent;border-left:4px solid #0d48bd}.admonition.notify .admonition-header{background:rgba(13,72,189,0.1);color:#0d48bd}.admonition.question{background:transparent;border-left:4px solid #179299}.admonition.question .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.quote{background:transparent;border-left:4px solid #7287fd}.admonition.quote .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.success{background:transparent;border-left:4px solid #40a02b}.admonition.success .admonition-header{background:rgba(64,160,43,0.1);color:#40a02b}.admonition.task{background:transparent;border-left:4px solid #8839ef}.admonition.task .admonition-header{background:rgba(136,57,239,0.1);color:#8839ef}.admonition.tip{background:transparent;border-left:4px solid #179299}.admonition.tip .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.warning{background:transparent;border-left:4px solid #df8e1d}.admonition.warning .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}
--- a/jupyterhub_volumes/web/obidoc/docs/about/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/about/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/advanced/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Advanced tools on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/advanced/</link>
-    <description>Recent content in Advanced tools on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/advanced/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Sequence alignments on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/alignments/</link>
-    <description>Recent content in Sequence alignments on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Exact alignment on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/</link>
-    <description>Recent content in Exact alignment on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/match.json
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/match.json
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/mismatch.json
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/mismatch.json
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/pairing_score.qmd
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/pairing_score.qmd
@@ -1,149 +0,0 @@
---
-title: "Untitled"
-format: html
-editor: visual
---
-
-```{r}
-library(tidyverse)
-library(plotly)
-library(matrixStats)
-```
-
-```{r}
-log_sum_exp <- function(a,b) {
-  m <- map2_dbl(a,b,max)
-  m + log(exp(a-m)+exp(b-m))
-}
-```
-
-$$
-\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
-$$
-
-```{r}
-log1m_exp <- function(b) {
-  if (any(b >= 0)) {
-    stop(glue::glue("b must be negative (b={b})"))
-  }
-  return(log(-expm1(b)))  # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
-}
-```
-
-$$
-\log(e^a - e^b) = a + \log(1 - e^{b-a})
-$$
-
-```{r}
-log_diff_exp <- function(a, b) {
-  # Vérifier si a > b pour éviter des résultats indéfinis
-  if (any(a < b)) {
-    stop(glue::glue("Erreur : a ({a}) doit etre strictement sup<75>rieur <20> b ({b}) pour que e^a - e^b soit positif."))
-  }
-  
-  # Calculer log(e^a - e^b) de manière stable
-  ifelse(a == b, -Inf,a + log1m_exp(b-a))
-}
-```
-
-$$
-P_{error} = 10^{-\frac{Q}{10}}
-$$
-
-$$
-\begin{aligned}
-q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
-q_R &= -\frac{Q_R}{10} \cdot \log(10) \\ 
-P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
-&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
-&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
-&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
-&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
-&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
-\end{aligned}
-$$
-
-```{r}
-Pm_match_observed <- function(Q_F, Q_R) {
-  l10 <- log(10)
-  l3 <- log(3)
-  l4 <- log(4)
-
-  q_F <- -Q_F/10*l10
-  q_R <- -Q_R/10*l10
-  
-  term1 <- log_sum_exp(q_F,q_R)
-  term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
-  
-  log1m_exp(term2)
-}
-```
-
-$$
-\begin{aligned}
-P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
-&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
-&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
-&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
-\end{aligned}
-$$
-
-```{r}
-Pm_mismatch_observed <- function(Q_F, Q_R) {
-  l10 <- log(10)
-  l3 <- log(3)
-  l4 <- log(4)
-
-  q_F <- -Q_F/10*l10
-  q_R <- -Q_R/10*l10
-  
-  term1 <- log_sum_exp(q_F,q_R)
-  log_diff_exp(term1,q_F+q_R) - l4
-}
-```
-
-```{r}
-score_match_observed <- function(Q_F, Q_R) {
-  Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R)) 
-}
-
-score_mismatch_observed <- function(Q_F, Q_R) {
-   Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R)) 
-}
-```
-
-```{r}
-scores <- expand_grid(QF=0:40,QR=0:40) %>%
-  mutate(score_match_observed = round(score_match_observed(QF,QR),2),
-         score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
-```
-
-```{r}
-plot_match <- plot_ly(scores, 
-        x=~QF, y=~QR, z=~score_match_observed, 
-        type="mesh3d") %>%
-    layout(
-        plot_bgcolor = "#bababa",
-        scene = list(
-            xaxis = list(title = "Q forward read"),   # Change x/y/z axis title
-            yaxis = list(title = "Q reverse read"),
-            zaxis = list(title = "Score match")))
-```
-
-```{r}
-plot_mismatch <- plot_ly(scores, 
-        x=~QF, y=~QR, z=~score_mismatch_observed, 
-        type="mesh3d") %>%
-    layout(
-        plot_bgcolor = "#bababa",
-        scene = list(
-            xaxis = list(title = "Q forward read"),   # Change x/y/z axis title
-            yaxis = list(title = "Q reverse read"),
-            zaxis = list(title = "Score mismatch")))
-```
-
-```{r}
-write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
-write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
-
-```
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/fasta_dotplot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/fasta_dotplot.png
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>The FASTA-like alignment on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/</link>
-    <description>Recent content in The FASTA-like alignment on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Basics on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/basics/</link>
-    <description>Recent content in Basics on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/basics/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Demultiplexing samples on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/demultiplexing/</link>
-    <description>Recent content in Demultiplexing samples on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/demultiplexing/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Experimentals on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/experimental/</link>
-    <description>Recent content in Experimentals on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/experimental/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/index.xml
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>The OBITools4 commands on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/</link>
-    <description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/index.xml" rel="self" type="application/rss+xml" />
-    <item>
-      <title>Glossary of tags</title>
-      <link>http://metabar:8888/obidoc/docs/commands/tags/</link>
-      <pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
-      <guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
-      <description>&lt;h1 id=&#34;glossary-of-tags&#34;&gt;&#xA;  Glossary of tags&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#glossary-of-tags&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h1&gt;&#xA;&lt;h3 id=&#34;--d--&#34;&gt;&#xA;  - D -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--d--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;definition&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;text information about the sequence present in the original sequence file.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;direction&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3 id=&#34;--f--&#34;&gt;&#xA;  - F -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--f--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_error&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Number of mismatch between forward primer and priming site&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_match&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer priming site sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_primer&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;</description>
-    </item>
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Shared command options on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/options/</link>
-    <description>Recent content in Shared command options on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/options/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/two_sequences.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/two_sequences.fasta
@@ -1,6 +0,0 @@
->AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
-ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
-ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
-agcttaaaactcaaaggacctggcagttctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/others/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/others/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Others on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/others/</link>
-    <description>Recent content in Others on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/others/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/tags/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/taxonomy/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Taxonomy on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/commands/taxonomy/</link>
-    <description>Recent content in Taxonomy on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/commands/taxonomy/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ecoPCRFormat
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ecoPCRFormat
@@ -1,604 +0,0 @@
-#!/usr/bin/env python3
-
-import re
-import gzip
-import struct
-import sys
-import time
-import getopt
-from functools import cmp_to_key
-
-_dbenable=False
-
-#####
-#
-#
-# Generic file function
-#
-#
-#####
-
-def universalOpen(file):
-    if isinstance(file,str):
-        if file[-3:] == '.gz':
-            rep = gzip.open(file)
-        else:
-            rep = open(file)
-    else:
-        rep = file
-    return rep
-
-def universalTell(file):
-    if isinstance(file, gzip.GzipFile):
-        file=file.myfileobj
-    return file.tell()
-
-def fileSize(file):
-    if isinstance(file, gzip.GzipFile):
-        file=file.myfileobj
-    pos = file.tell()
-    file.seek(0,2)
-    length = file.tell()
-    file.seek(pos,0)
-    return length
-
-def progressBar(pos,max,reset=False,delta=[]):
-    if reset:
-        del delta[:]
-    if not delta:
-        delta.append(time.time())
-        delta.append(time.time())
-
-    delta[1]=time.time()
-    elapsed = delta[1]-delta[0]
-    percent = float(pos)/max * 100
-    remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
-    bar = '#' * int(percent/2)
-    bar+= '|/-\\-'[pos % 5]
-    bar+= ' ' * (50 - int(percent/2))
-    sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
-
-#####
-#
-#
-# NCBI Dump Taxonomy reader
-#
-#
-#####
-
-def endLessIterator(endedlist):
-    for x in endedlist:
-        yield x
-    while(1):
-        yield endedlist[-1]
-   
-class ColumnFile(object):
-    
-    def __init__(self,stream,sep=None,strip=True,types=None):
-        if isinstance(stream,str):
-            self._stream = open(stream)
-        else:
-            try: 
-                iter(stream)
-                self._stream = stream
-            except TypeError:    
-                raise ValueError('stream must be string or an iterator')
-        self._delimiter=sep
-        self._strip=strip
-        if types:
-            self._types=[x for x in types]
-            for i in range(len(self._types)):
-                if self._types[i] is bool:
-                    self._types[i]=ColumnFile.str2bool
-        else:
-            self._types=None
-            
-    def str2bool(x):
-        return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
-                    
-    str2bool = staticmethod(str2bool)
-            
-        
-    def __iter__(self):
-        return self
-    
-    def __next__(self):
-        ligne = next(self._stream)
-        data = ligne.split(self._delimiter)
-        if self._strip or self._types:
-            data = [x.strip() for x in data]
-        if self._types:
-            it = endLessIterator(self._types)
-            data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
-        return data
-    
-def taxonCmp(t1,t2):
-    if t1[0] < t2[0]:
-        return -1
-    elif t1[0] > t2[0]:
-        return +1
-    return 0
-
-def bsearchTaxon(taxonomy,taxid):
-    taxCount = len(taxonomy)
-    begin = 0
-    end   = taxCount 
-    oldcheck=taxCount
-    check = int(begin + end / 2)
-    while check != oldcheck and taxonomy[check][0]!=taxid :
-        if taxonomy[check][0] < taxid:
-            begin=check
-        else:
-            end=check
-        oldcheck=check
-        check = int((begin + end) / 2)
-        
-        
-    if taxonomy[check][0]==taxid:
-        return check
-    else:
-        return None
-        
-    
-    
-def readNodeTable(file):
-
-    file = universalOpen(file)
-    
-    nodes = ColumnFile(file, 
-                       sep='|', 
-                       types=(int,int,str,
-                              str,str,bool,
-                              int,bool,int,
-                              bool,bool,bool,str))
-    print("Reading taxonomy dump file...", file=sys.stderr)
-    taxonomy=[[n[0],n[2],n[1]] for n in nodes]
-    print("List all taxonomy rank...", file=sys.stderr)    
-    ranks =list(set(x[1] for x in taxonomy))
-    ranks.sort()
-    ranks = {rank: index for index, rank in enumerate(ranks)}
-    
-    print("Sorting taxons...", file=sys.stderr)
-    taxonomy.sort(key=lambda x: x[0])
-
-    print("Indexing taxonomy...", file=sys.stderr)
-    index = {}
-    for t in taxonomy:
-        index[t[0]]=bsearchTaxon(taxonomy, t[0])
-    
-    print("Indexing parent and rank...", file=sys.stderr)
-    for t in taxonomy:
-        t[1]=ranks[t[1]]
-        t[2]=index[t[2]]
-        
-        
-    return taxonomy,ranks,index
-
-def nameIterator(file):
-    file = universalOpen(file)
-    names = ColumnFile(file, 
-                       sep='|', 
-                       types=(int,str,
-                              str,str))
-    for taxid,name,unique,classname,white in names:
-        yield taxid,name,classname
-        
-def mergedNodeIterator(file):
-    file = universalOpen(file)
-    merged = ColumnFile(file, 
-                       sep='|', 
-                       types=(int,int,str))
-    for taxid,current,white in merged:
-            yield taxid,current
-    
-def deletedNodeIterator(file):
-    file = universalOpen(file)
-    deleted = ColumnFile(file, 
-                       sep='|', 
-                       types=(int,str))
-    for taxid,white in deleted:
-            yield taxid
-    
-def readTaxonomyDump(taxdir):
-    taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
-    
-    print("Adding scientific name...", file=sys.stderr)
-
-    alternativeName=[]
-    for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
-        alternativeName.append((name,classname,index[taxid]))
-        if classname == 'scientific name':
-            taxonomy[index[taxid]].append(name)
-        
-    print("Adding taxid alias...", file=sys.stderr)
-    for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
-        index[taxid]=index[current]
-    
-    print("Adding deleted taxid...", file=sys.stderr)
-    for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
-        index[taxid]=None
-    
-    return taxonomy,ranks,alternativeName,index
-
-#####
-#
-#
-#  Genbank/EMBL sequence reader
-#
-#
-#####
-
-def entryIterator(file):
-    file = universalOpen(file)
-    rep =[]
-    ligne = file.readline()
-    while ligne:
-        rep.append(ligne)
-        if ligne == '//\n':
-            rep = ''.join(rep)
-            yield rep
-            rep = []
-        ligne = file.readline()
-            
-def fastaEntryIterator(file):
-    file = universalOpen(file)
-    rep =[]
-    ligne =  file.readline()
-    while ligne:
-        if ligne[0] == '>' and rep:
-            rep = ''.join(rep)
-            yield rep
-            rep = []
-        rep.append(ligne)
-        ligne = file.readline()
-
-    if rep:
-        rep = ''.join(rep)
-        yield rep
-    
-_cleanSeq = re.compile('[ \n0-9]+')
-            
-def cleanSeq(seq):
-    return _cleanSeq.sub('',seq)
-    
-    
-_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)   
-_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)   
-_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)  
-_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
-  
-def genbankEntryParser(entry):
-    Id = _gbParseID.findall(entry)[0]
-    De = ' '.join(_gbParseDE.findall(entry)[0].split())
-    Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
-    try:
-        Tx = int(_gbParseTX.findall(entry)[0])
-    except IndexError:
-        Tx = None
-    return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
-
-######################
-
-_cleanDef = re.compile('[\nDE]')
-
-def cleanDef(definition):
-    return _cleanDef.sub('',definition)
-
-_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)   
-_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)   
-_emblParseSQ = re.compile('(?<=^  ).+?(?=^//$)',re.MULTILINE+re.DOTALL)  
-_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
-
-def emblEntryParser(entry):
-    Id = _emblParseID.findall(entry)[0]
-    De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
-    Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
-    try:
-        Tx = int(_emblParseTX.findall(entry)[0])
-    except IndexError:
-        Tx = None
-    return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
-
-
-######################
-
-_fastaSplit=re.compile(';\\W*')
-
-def parseFasta(seq):
-    seq=seq.split('\n')
-    title = seq[0].strip()[1:].split(None,1)
-    id=title[0]
-    if len(title) == 2:
-        field = _fastaSplit.split(title[1])
-    else:
-        field=[]
-    info = dict(x.split('=',1) for x in field if '=' in x)
-    definition = ' '.join([x for x in field if '=' not in x])
-    seq=(''.join([x.strip() for x in seq[1:]])).upper()   
-    return id,seq,definition,info
-
-  
-def fastaEntryParser(entry):
-    id,seq,definition,info = parseFasta(entry)
-    Tx = info.get('taxid',None)   
-    if Tx is not None:
-        match = re.search(r'taxon:(\d+)', Tx)
-        if match:
-            Tx = match.group(1)
-        Tx=int(Tx)
-    return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
-    
-
-def sequenceIteratorFactory(entryParser,entryIterator):
-    def sequenceIterator(file):
-        for entry in entryIterator(file):
-            yield entryParser(entry)
-    return sequenceIterator
-
-
-def taxonomyInfo(entry,connection):
-    taxid = entry['taxid']
-    curseur = connection.cursor()
-    curseur.execute("""
-                        select taxid,species,genus,family,
-                               taxonomy.scientificName(taxid) as sn,
-                               taxonomy.scientificName(species) as species_sn,
-                               taxonomy.scientificName(genus) as genus_sn,
-                               taxonomy.scientificName(family) as family_sn
-                        from
-                            (   
-                             select alias                      as taxid,
-                               taxonomy.getSpecies(alias) as species,
-                               taxonomy.getGenus(alias)   as genus,
-                               taxonomy.getFamily(alias)  as family
-                                from taxonomy.aliases
-                               where id=%d ) as tax
-                    """ % taxid)
-    rep = curseur.fetchone()
-    entry['current_taxid']=rep[0]
-    entry['species']=rep[1]
-    entry['genus']=rep[2]
-    entry['family']=rep[3]
-    entry['scientific_name']=rep[4]
-    entry['species_sn']=rep[5]
-    entry['genus_sn']=rep[6]
-    entry['family_sn']=rep[7]
-    return entry
-    
-#####
-#
-#
-# Binary writer
-#
-#
-#####
-    
-def ecoSeqPacker(sq):
-    
-    compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
-    cptseqlength  = len(compactseq)
-    delength   = len(sq['definition'])
-    
-    totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
-    
-    packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
-                         totalSize,
-                         sq['taxid'],
-                         bytes(sq['id'],"ascii"),
-                         delength,
-                         len(sq['sequence']),
-                         cptseqlength,
-                         bytes(sq['definition'],"ascii"),
-                         compactseq)
-    
-    assert len(packed) == totalSize+4, "error in sequence packing"
-    
-    return packed
-
-def ecoTaxPacker(tx):
-    
-    namelength = len(tx[3])
-    
-    totalSize = 4 + 4 + 4 + 4 + namelength
-    
-    packed = struct.pack('> I I I I I %ds' % namelength, 
-                         totalSize, 
-                         tx[0],
-                         tx[1],
-                         tx[2], 
-                         namelength,
-                         bytes(tx[3],"ascii"))
-    
-    return packed
-
-def ecoRankPacker(rank):
-    
-    namelength = len(rank)
-    
-    packed = struct.pack('> I %ds' % namelength,
-                         namelength,
-                         bytes(rank, 'ascii'))
-    
-    return packed
-                
-def ecoNamePacker(name):
-    
-    namelength = len(name[0])
-    classlength= len(name[1])
-    totalSize =  namelength + classlength + 4 + 4 + 4 + 4
-    
-    packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
-                         totalSize,
-                         int(name[1]=='scientific name'),
-                         namelength,
-                         classlength,
-                         name[2],
-                         bytes(name[0], 'ascii'),
-                         bytes(name[1], 'ascii'))
-    
-    return packed
-    
-def ecoSeqWriter(file,input,taxindex,parser):
-    output = open(file,'wb')
-    input  = universalOpen(input)
-    inputsize = fileSize(input)
-    entries = parser(input)
-    seqcount=0
-    skipped = []
-
-    output.write(struct.pack('> I',seqcount))
-    
-    progressBar(1, inputsize,reset=True)
-    for entry in entries:
-        if entry['taxid'] is not None:
-            try:
-                entry['taxid']=taxindex[entry['taxid']]
-            except KeyError:
-                entry['taxid']=None
-            if entry['taxid'] is not None:
-                seqcount+=1
-                output.write(ecoSeqPacker(entry))
-            else:
-                skipped.append(entry['id'])
-            where = universalTell(input)
-            progressBar(where, inputsize)
-            print(" Readed sequences : %d     " % seqcount, end=' ', file=sys.stderr)
-        else:
-            skipped.append(entry['id'])
-        
-    print(file=sys.stderr)
-    output.seek(0,0)
-    output.write(struct.pack('> I',seqcount))
-    
-    output.close()
-    return skipped
-        
-
-def ecoTaxWriter(file,taxonomy):
-    output = open(file,'wb')
-    output.write(struct.pack('> I',len(taxonomy)))
-    
-    for tx in taxonomy:
-        output.write(ecoTaxPacker(tx))
-
-    output.close()
-    
-def ecoRankWriter(file,ranks):
-    output = open(file,'wb')
-    output.write(struct.pack('> I',len(ranks)))
-
-    rankNames = list(ranks.keys())
-    rankNames.sort()
-    
-    for rank in rankNames:
-        output.write(ecoRankPacker(rank))
-
-    output.close()
-
-def nameCmp(n1,n2):
-    name1=n1[0].upper()
-    name2=n2[0].upper()
-    if name1 < name2:
-        return -1
-    elif name1 > name2:
-        return 1
-    return 0
-
-
-def ecoNameWriter(file,names):
-    output = open(file,'wb')
-    output.write(struct.pack('> I',len(names)))
-
-    names.sort(key=lambda x:x[0].upper())
-    
-    for name in names:
-        output.write(ecoNamePacker(name))
-
-    output.close()
-    
-def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
-    
-    ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
-    ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
-    ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
-  
-    filecount = 0
-    for filename in seqFileNames:
-        filecount+=1
-        sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount), 
-                     filename, 
-                     taxonomy[3], 
-                     parser)
-        if sk:
-            print("Skipped entry :", file=sys.stderr)
-            print(sk, file=sys.stderr)
-        
-def ecoParseOptions(arguments):
-    opt = {
-            'prefix' : 'ecodb',
-            'taxdir' : 'taxdump',
-            'parser' : sequenceIteratorFactory(genbankEntryParser,
-                                                  entryIterator)
-           }
-    
-    o,filenames = getopt.getopt(arguments,
-                                'ht:T:n:gfe',
-                                ['help',
-                                 'taxonomy=',
-                                 'taxonomy_db=',
-                                 'name=',
-                                 'genbank',
-                                 'fasta',
-                                 'embl'])
-    
-    for name,value in o:
-        if name in ('-h','--help'):
-            printHelp()
-            exit()
-        elif name in ('-t','--taxonomy'):
-            opt['taxmod']='dump'
-            opt['taxdir']=value
-        elif name in ('-T','--taxonomy_db'):
-            opt['taxmod']='db'
-            opt['taxdb']=value
-        elif name in ('-n','--name'):
-            opt['prefix']=value
-        elif name in ('-g','--genbank'):
-            opt['parser']=sequenceIteratorFactory(genbankEntryParser,
-                                                  entryIterator)
-
-        elif name in ('-f','--fasta'):
-            opt['parser']=sequenceIteratorFactory(fastaEntryParser,
-                                                  fastaEntryIterator)
-            
-        elif name in ('-e','--embl'):
-            opt['parser']=sequenceIteratorFactory(emblEntryParser,
-                                                  entryIterator)
-        else:
-            raise ValueError('Unknown option %s' % name)
-
-    return opt,filenames
-
-def printHelp():
-    print("-----------------------------------")
-    print(" ecoPCRFormat.py")
-    print("-----------------------------------")
-    print("ecoPCRFormat.py [option] <argument>")
-    print("-----------------------------------")
-    print("-e    --embl        :[E]mbl format")
-    print("-f    --fasta       :[F]asta format")
-    print("-g    --genbank     :[G]enbank format")
-    print("-h    --help        :[H]elp - print this help")
-    print("-n    --name        :[N]ame of the new database created")
-    print("-t    --taxonomy    :[T]axonomy - path to the taxonomy database")
-    print("                    :bcp-like dump from GenBank taxonomy database.")
-    print("-----------------------------------")
-
-if __name__ == '__main__':
-    
-    opt,filenames = ecoParseOptions(sys.argv[1:])
-    
-    taxonomy = readTaxonomyDump(opt['taxdir'])
-    
-    ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
-    
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Designing new barcodes on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
-    <description>Recent content in Designing new barcodes on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ncbi-ftp.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/ncbi-ftp.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
@@ -1,103 +0,0 @@
-SHELL := /bin/bash
-FTPNCBI=ftp.ncbi.nlm.nih.gov
-GBURL=https://$(FTPNCBI)/genbank
-GBRELEASE_URL=$(GBURL)/GB_Release_Number
-
-TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
-
-GBRELEASE:=$(shell curl $(GBRELEASE_URL))
-
-GBDIV_ALL:=$(shell curl -L ${GBURL} \
-                  | grep -E 'gb.+\.seq\.gz' \
-				  | sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
-				  | sort \
-				  | uniq)
-
-GBDIV=bct inv mam phg pln pri rod vrl vrt
-DIRECTORIES=fasta fasta_fgs
-
-GBFILE_ALL:=$(shell curl -L ${GBURL} \
-					| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
-					| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
-
-
-SUFFIXES += .d
-NODEPS:=clean taxonomy
-DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
-
-ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
-    #Chances are, these files don't exist.  GMake will create them and
-    #clean up automatically afterwards
-    -include $(DEPFILES)
-endif
-
-
-all: depends directories FORCE
-	@make downloads
-
-downloads: taxonomy fasta_files 
-	@echo Genbank Release number $(GBRELEASE)
-	@echo all divisions : $(GBDIV_ALL)
-
-FORCE:
-	@sleep 1
-
-.PHONY: all directories depends taxonomy fasta_files FORCE
-
-depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
-
-division: $(GBDIV)
-
-taxonomy: directories Release_$(GBRELEASE)/taxonomy
-
-directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp 
-
-Release_$(GBRELEASE):
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
-	@echo Create depends directory
-	@mkdir -p Release_$(GBRELEASE)/depends
-	@for f in ${GBFILE_ALL} ; do \
-	            echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
-				echo -e "\t@echo Downloading file : $$f..." ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
-				echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@"  ; \
-				echo ; \
-				div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
-				fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
-				fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
-				fasta_files="$$fasta_files $$fasta" ; \
-				fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
-				echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
-				echo -e "\t@echo converting file : \$$< in fasta" ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
-				echo -e "\t@obiconvert -Z --fasta-output --skip-empty  \\" ; \
-				echo -e "\t            Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
-				echo -e "\t            && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@  \\" ; \
-				echo -e "\t            && rm -f Release_$(GBRELEASE)/tmp/$$f  \\" ; \
-				echo -e "\t            || rm -f \$$@" ; \
-				echo -e "\t@echo conversion of $$@ done." ; \
-				echo ; \
-				done > $@ ; \
-				echo >> $@ ; \
-				echo "fasta_files: $$fasta_files" >> $@ ; 
-
-Release_$(GBRELEASE)/taxonomy: 
-	mkdir -p $@
-	curl -iL $(TAXOURL) \
-	| tar -C $@ -zxf -  
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Analysing an Illumina data set on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
-    <description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/length-plot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/length-plot.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/unidentified.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/unidentified.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_1_percent.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_1_percent.fasta
@@ -1,26 +0,0 @@
->HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
-tttt
->HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple.fasta
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple_clean.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_simple_clean.fasta
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_short.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_short.fasta
@@ -1,24 +0,0 @@
->HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_singleton.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_no_singleton.fasta
@@ -1,329 +0,0 @@
->HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
-ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:63:4595:15643#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
-ttagccctaaacataagctattccataacaaaataattcgccagagtactaccggcaata
-gcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:7:8807:7823#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:19171:11413#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:8:6794:4925#0/1_sub[28..127]":"(t)->(g)@38"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
-ttagccctaaacacaagtaattaatataacaaaagtagtcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:44:5008:2115#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:53:16956:10563#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
-ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:54:10323:7022#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
-ttagccctaaacacaaataattatataaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:45:7460:13396#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttatgcccgt
->HELIUM_000100422_612GNAAXX:7:58:8409:9911#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:100:18844:15930#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaagcgcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:29:9723:20435#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
-ttagccctaaacacaaataattacacaaacaaaattgttcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:43:4660:16319#0/1_sub[28..126] {"count":22,"merged_sample":{"26a_F040644":22},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":42}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:103:11045:3860#0/1_sub[28..127] {"count":4,"merged_sample":{"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":4}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaagggcttggcggtgctttatgccctt
->HELIUM_000100422_612GNAAXX:7:67:10944:19430#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
-ttagccctaaacacaagtaattaatataacaaaattattcgtcagagtactaccggcaat
-agcttaaaactcaaaggacgtggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:56:6962:17278#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":7}}
-ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:60:13553:20530#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-atgttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:35:13167:18371#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccggagaactactaggaaca
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:105:1895:7593#0/1_sub[28..127] {"count":11,"merged_sample":{"29a_F260619":11},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":13}}
-ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
-agcttaaaactcaaaggacctggcggtgcttcatatccct
->HELIUM_000100422_612GNAAXX:7:118:15661:12736#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
-ttagccctaaacacaagtaattaatataacaaaattatccgcaagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:30:8391:13152#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
-agcccaaaactcaaaggacttggcggtgcttcacaccctt
->HELIUM_000100422_612GNAAXX:7:95:14375:10838#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":5}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:82:13334:18499#0/1_sub[28..127] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":10}}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:11272:1128#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactactagcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:7:6016:14767#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacgtctagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:9:8337:12329#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":6}}
-ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:15:12854:18952#0/1_sub[28..126] {"count":10,"merged_sample":{"29a_F260619":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":16}}
-ttagccctaaacataagctattccataacaaaattattcgccagagtactaccggcaata
-gcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:1:4513:20277#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaaccattctataacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:57:18237:6765#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
-ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:119:8691:15994#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
-agcttaaaacgcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:6:1739:11421#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaagaatgttcgctagagtactactagcaaca
-gcctgacactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:73:17136:17728#0/1_sub[28..127] {"count":6,"merged_sample":{"13a_F730603":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
-ctagccttaaacacaaatagttatgcaaacaaaattattcgccagagtactaccggcaac
-agcccaaaactcaaaggacttggcggtgcttcacaccctt
->HELIUM_000100422_612GNAAXX:7:76:9874:3117#0/1_sub[28..127] {"count":9,"merged_sample":{"29a_F260619":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:18:16679:15889#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
-ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:52:6908:8410#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":10}}
-ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:71:13461:7411#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagaagactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
-tttt
->HELIUM_000100422_612GNAAXX:7:47:6989:13864#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:72:8941:18482#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
-gcctaaaactcaaaggacttggtggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:25:10818:13742#0/1_sub[28..133] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
-ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
-agcaacagcttaaaactcaaaggacttggtggtgctttctacccct
->HELIUM_000100422_612GNAAXX:7:70:11509:6042#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
-ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:46:4342:17317#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
-ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
-gcttaaaactcaaaggacttggcggtgccttacgtccct
->HELIUM_000100422_612GNAAXX:7:111:17844:17230#0/1_sub[28..126] {"count":13,"merged_sample":{"26a_F040644":13},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":17}}
-ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacgtggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127] {"count":15,"merged_sample":{"13a_F730603":15},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":15}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgcttcacaccctt
->HELIUM_000100422_612GNAAXX:7:34:2640:2539#0/1_sub[28..127] {"count":19,"merged_sample":{"29a_F260619":19},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":25}}
-ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:71:18891:9661#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacgtggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:26:16553:1613#0/1_sub[77..81] {"count":38,"merged_sample":{"13a_F730603":38},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":38}}
-caata
->HELIUM_000100422_612GNAAXX:7:45:5732:11220#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggtggtgctttctacccct
->HELIUM_000100422_612GNAAXX:7:1:14254:1103#0/1_sub[28..126] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:50:17151:20608#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:96:13203:2879#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":6}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
-agcccaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:78:18041:18996#0/1_sub[28..126] {"count":13,"merged_sample":{"13a_F730603":9,"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s"},"obiclean_weight":{"13a_F730603":9,"15a_F730814":4}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:80:18387:10166#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:100:14685:15065#0/1_sub[28..127]":"(a)->(t)@24","HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127]":"(t)->(g)@71"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaacgcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:54:10113:12172#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":4,"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":5,"29a_F260619":4}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:97:17822:18365#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
-agcttaaaactcaaaggacttggcggtgctttatcccctt
->HELIUM_000100422_612GNAAXX:7:87:6328:12406#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:7:4611:13145#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:78:6346:5817#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
-ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
-agcccaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:7:15122:17310#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:94:6384:20392#0/1_sub[28..127]":"(a)->(t)@52"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:27:7695:17738#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:48:15379:13773#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
-ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:117:16246:17184#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":10}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:87:11044:6323#0/1_sub[28..126] {"count":69,"merged_sample":{"26a_F040644":69},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":84}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:40:12248:18615#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
-ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:7:6470:13562#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:72:11850:15705#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:82:8566:4827#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":9}}
-ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
-gcctaaaactcaaaggacttggtggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:43:16297:17399#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
-ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:7:15117:2564#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:90:4058:17862#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:43:13909:1377#0/1_sub[28..126] {"count":10,"merged_sample":{"26a_F040644":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":14}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
-gcctaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:36:3584:21256#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
-ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttatgccctt
->HELIUM_000100422_612GNAAXX:7:80:13357:2959#0/1_sub[74..81] {"count":12,"merged_sample":{"29a_F260619":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
-ccgatagg
->HELIUM_000100422_612GNAAXX:7:70:8097:4516#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
-gcctaaaactcaaaggacttggcagtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:7:8746:5790#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:8:9165:18915#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:85:7323:6139#0/1_sub[28..126] {"count":9,"merged_sample":{"26a_F040644":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":16}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:23:6103:3418#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
-ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:107:2103:10677#0/1_sub[28..127] {"count":20,"merged_sample":{"13a_F730603":20},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":22}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:1:15993:20360#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacctgcaat
-agcttaaaactcaaaggacttggcggtgctttatgccctt
->HELIUM_000100422_612GNAAXX:7:103:1205:6990#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
-ttagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:111:2380:10482#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaata
-gcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:76:10530:11312#0/1_sub[28..126] {"count":43,"merged_sample":{"26a_F040644":43},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":69}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:40:15984:4911#0/1_sub[28..126] {"count":16,"merged_sample":{"26a_F040644":16},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":30}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:109:19171:17424#0/1_sub[28..126] {"count":2,"merged_sample":{"13a_F730603":1,"26a_F040644":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126]":"(a)->(t)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s","26a_F040644":"i"},"obiclean_weight":{"13a_F730603":1,"26a_F040644":1}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggacttctagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:77:17898:19592#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
-ttagccctaaacacaagtaattaatataacaaaataattcgccagaggactactagcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:32:4908:16517#0/1_sub[78..81] {"count":7,"merged_sample":{"29a_F260619":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
-ccgc
->HELIUM_000100422_612GNAAXX:7:100:8022:19461#0/1_sub[28..127] {"count":5,"merged_sample":{"29a_F260619":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":11}}
-ttagccctaaacacaagtaattaatataacaaaataattcgccagagaactactagcaac
-agattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:59:2390:15297#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
-gcctaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:98:10839:20244#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
-ttagccctaaacataaacattcaataaacaaggatgttcgccagagtactactagcaatg
-gcctaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:34:13086:6440#0/1_sub[28..127] {"count":14,"merged_sample":{"13a_F730603":14},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":18}}
-ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
-agcccaaaactcaaaggacttggcggtgcttcacaccctt
->HELIUM_000100422_612GNAAXX:7:73:10944:14101#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":3}}
-ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:61:17561:21218#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
-gcttaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:93:7569:17305#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaatcagtctataacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:55:11954:15731#0/1_sub[28..126] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:54:15067:12524#0/1_sub[28..126] {"count":26,"merged_sample":{"26a_F040644":26},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":49}}
-ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:6:10451:2548#0/1_sub[28..126] {"count":12,"merged_sample":{"26a_F040644":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":15}}
-ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaatg
-gcctaaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:23:10872:20213#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
-ttagccctaaacataaatcattctataacaaaataattcgccggagaactactagcaaca
-gcttaaaactcaaaggacttggcggtgccttacgtccct
->HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:98:6034:5203#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
-ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:70:2429:19509#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgccttacgtccct
->HELIUM_000100422_612GNAAXX:7:65:1843:2567#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
-ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:92:1339:19811#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
-ttagccctaaacacaagtaattacacaaacaaaattgttcacaagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:15:13855:1746#0/1_sub[28..127] {"count":3,"merged_sample":{"15a_F730814":2,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:7:14405:19348#0/1_sub[28..127]":"(t)->(g)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":3,"29a_F260619":1}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgcgaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:7:7092:11003#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacgtccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_taxo.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_taxo.fasta
@@ -1,24 +0,0 @@
->HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
@@ -1,24 +0,0 @@
->seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
@@ -1,9 +0,0 @@
-id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
-seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
-seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
-seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
-seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
-seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
-seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
-seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
-seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_occurrency.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_occurrency.csv
@@ -1,6 +0,0 @@
-id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
-29a_F260619,0,337,0,0,105,5789,376,1
-15a_F730814,0,0,0,0,0,8822,0,5
-13a_F730603,0,0,8039,0,0,0,0,17
-26a_F040644,12205,0,0,202,12,0,0,468
-
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_minimal.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_minimal.fasta
@@ -1,24 +0,0 @@
->HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
-gcctgaaactcaaaggacttggcggtgctttacatccct
->HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
-ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
-ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
-ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
->HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
-ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
-gattaaacctcaaaggacttggcagtgctttatacccct
->HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
-ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
-agcttaaaactcaaaggacttggcggtgctttataccctt
->HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
-ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
-gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/variants-plot.png
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/variants-plot.png
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/db_v05_r117.fasta.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/db_v05_r117.fasta.gz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Cookbook on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/</link>
-    <description>Recent content in Cookbook on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/Makefile
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/Makefile
@@ -1,102 +0,0 @@
-SHELL := /bin/bash
-FTPNCBI=ftp.ncbi.nlm.nih.gov
-GBURL=https://$(FTPNCBI)/genbank
-GBRELEASE_URL=$(GBURL)/GB_Release_Number
-
-TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
-
-GBRELEASE:=$(shell curl $(GBRELEASE_URL))
-
-GBDIV_ALL:=$(shell curl -L ${GBURL} \
-                  | grep -E 'gb.+\.seq\.gz' \
-				  | sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
-				  | sort \
-				  | uniq)
-
-GBDIV=bct inv mam phg pln pri rod vrl vrt
-DIRECTORIES=fasta fasta_fgs
-
-GBFILE_ALL:=$(shell curl -L ${GBURL} \
-					| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
-					| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
-
-
-SUFFIXES += .d
-NODEPS:=clean taxonomy
-DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
-
-ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
-    #Chances are, these files don't exist.  GMake will create them and
-    #clean up automatically afterwards
-    -include $(DEPFILES)
-endif
-
-
-all: depends directories FORCE
-	@make downloads
-
-downloads: taxonomy fasta_files 
-	@echo Genbank Release number $(GBRELEASE)
-	@echo all divisions : $(GBDIV_ALL)
-
-FORCE:
-
-.PHONY: all directories depends taxonomy fasta_files FORCE
-
-depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
-
-division: $(GBDIV)
-
-taxonomy: directories Release_$(GBRELEASE)/taxonomy
-
-directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp 
-
-Release_$(GBRELEASE):
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
-	@mkdir -p $@ 
-	@echo Create $@ directory
-
-Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
-	@echo Create depends directory
-	@mkdir -p Release_$(GBRELEASE)/depends
-	@for f in ${GBFILE_ALL} ; do \
-	            echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
-				echo -e "\t@echo Downloading file : $$f..." ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
-				echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@"  ; \
-				echo ; \
-				div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
-				fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
-				fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
-				fasta_files="$$fasta_files $$fasta" ; \
-				fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
-				echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
-				echo -e "\t@echo converting file : \$$< in fasta" ; \
-				echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
-				echo -e "\t@obiconvert -Z --fasta-output --skip-empty  \\" ; \
-				echo -e "\t            Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
-				echo -e "\t            && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@  \\" ; \
-				echo -e "\t            && rm -f Release_$(GBRELEASE)/tmp/$$f  \\" ; \
-				echo -e "\t            || rm -f \$$@" ; \
-				echo -e "\t@echo conversion of $$@ done." ; \
-				echo ; \
-				done > $@ ; \
-				echo >> $@ ; \
-				echo "fasta_files: $$fasta_files" >> $@ ; 
-
-Release_$(GBRELEASE)/taxonomy: 
-	mkdir -p $@
-	curl -iL $(TAXOURL) \
-	| tar -C $@ -zxf -  
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Prepare a local copy of Genbank on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
-    <description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Oxford Nanopore data analysis on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
-    <description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.xml
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Build a reference database on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
-    <description>Recent content in Build a reference database on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <lastBuildDate></lastBuildDate>
-    <atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>File formats on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/file_format/</link>
-    <description>Recent content in File formats on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/file_format/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/annotations/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/annotations/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/annotations/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/annotations/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Annotation of sequences on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/</link>
-    <description>Recent content in Annotation of sequences on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>CSV format on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/</link>
-    <description>Recent content in CSV format on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/two_sequences.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/two_sequences.fasta
@@ -1,6 +0,0 @@
->AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
-ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
-agcttaaaactcaaaggacttggcggtgctttatatccct
->AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
-ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
-agcttaaaactcaaaggacctggcagttctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/two_sequences.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/csv/two_sequences.fastq
@@ -1,8 +0,0 @@
-@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46} 
-ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
-+
-CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
-@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(A:02)->(G:30)":104,"(A:34)->(G:14)":64,"(C:02)->(A:30)":86,"(C:02)->(T:20)":108,"(C:27)->(G:32)":83,"(C:34)->(G:18)":57,"(T:02)->(G:26)":87,"(T:22)->(G:14)":66,"(T:29)->(G:11)":62,"(T:32)->(G:30)":48},"score":283,"score_norm":0.839,"seq_a_single":46,"seq_ab_match":52,"seq_b_single":46} 
-ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
-+
-CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/sequence_files/index.xml
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8" standalone="yes"?>
-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
-  <channel>
-    <title>Sequence file formats on OBITools4 documentation</title>
-    <link>http://metabar:8888/obidoc/docs/file_format/sequence_files/</link>
-    <description>Recent content in Sequence file formats on OBITools4 documentation</description>
-    <generator>Hugo</generator>
-    <language>en-us</language>
-    <atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/index.xml" rel="self" type="application/rss+xml" />
-  </channel>
-</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/taxonomy_file/csv_taxdump/betula_subtaxo.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/taxonomy_file/csv_taxdump/betula_subtaxo.csv
@@ -1,30 +0,0 @@
-taxid,parent,taxonomic_rank,scientific_name
-taxon:1 [root]@no rank,taxon:1 [root]@no rank,no rank,root
-taxon:131567 [cellular organisms]@no rank,taxon:1 [root]@no rank,no rank,cellular organisms
-taxon:2759 [Eukaryota]@superkingdom,taxon:131567 [cellular organisms]@no rank,superkingdom,Eukaryota
-taxon:33090 [Viridiplantae]@kingdom,taxon:2759 [Eukaryota]@superkingdom,kingdom,Viridiplantae
-taxon:35493 [Streptophyta]@phylum,taxon:33090 [Viridiplantae]@kingdom,phylum,Streptophyta
-taxon:131221 [Streptophytina]@subphylum,taxon:35493 [Streptophyta]@phylum,subphylum,Streptophytina
-taxon:3193 [Embryophyta]@clade,taxon:131221 [Streptophytina]@subphylum,clade,Embryophyta
-taxon:58023 [Tracheophyta]@clade,taxon:3193 [Embryophyta]@clade,clade,Tracheophyta
-taxon:78536 [Euphyllophyta]@clade,taxon:58023 [Tracheophyta]@clade,clade,Euphyllophyta
-taxon:58024 [Spermatophyta]@clade,taxon:78536 [Euphyllophyta]@clade,clade,Spermatophyta
-taxon:3398 [Magnoliopsida]@class,taxon:58024 [Spermatophyta]@clade,class,Magnoliopsida
-taxon:1437183 [Mesangiospermae]@clade,taxon:3398 [Magnoliopsida]@class,clade,Mesangiospermae
-taxon:71240 [eudicotyledons]@clade,taxon:1437183 [Mesangiospermae]@clade,clade,eudicotyledons
-taxon:91827 [Gunneridae]@clade,taxon:71240 [eudicotyledons]@clade,clade,Gunneridae
-taxon:1437201 [Pentapetalae]@clade,taxon:91827 [Gunneridae]@clade,clade,Pentapetalae
-taxon:71275 [rosids]@clade,taxon:1437201 [Pentapetalae]@clade,clade,rosids
-taxon:91835 [fabids]@clade,taxon:71275 [rosids]@clade,clade,fabids
-taxon:3502 [Fagales]@order,taxon:91835 [fabids]@clade,order,Fagales
-taxon:3514 [Betulaceae]@family,taxon:3502 [Fagales]@order,family,Betulaceae
-taxon:3504 [Betula]@genus,taxon:3514 [Betulaceae]@family,genus,Betula
-taxon:1685988 [Betula murrayana]@species,taxon:3504 [Betula]@genus,species,Betula murrayana
-taxon:361422 [Betula ovalifolia]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia
-taxon:1685972 [Betula x caerulea]@species,taxon:3504 [Betula]@genus,species,Betula x caerulea
-taxon:216986 [Betula schmidtii]@species,taxon:3504 [Betula]@genus,species,Betula schmidtii
-taxon:312791 [Betula michauxii]@species,taxon:3504 [Betula]@genus,species,Betula michauxii
-taxon:3015411 [Betula pamirica]@species,taxon:3504 [Betula]@genus,species,Betula pamirica
-taxon:312792 [Betula raddeana]@species,taxon:3504 [Betula]@genus,species,Betula raddeana
-taxon:216991 [Betula humilis]@species,taxon:3504 [Betula]@genus,species,Betula humilis
-taxon:2218489 [Betula ovalifolia x Betula ermanii]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia x Betula ermanii
--- a/jupyterhub_volumes/web/obidoc/docs/file_format/taxonomy_file/csv_taxdump/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/file_format/taxonomy_file/csv_taxdump/index.html
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Eric Coissac	2417959fbd	Add options to startup script	2025-11-26 09:47:20 +01:00
Eric Coissac	4e338bc1d4	Complete the documentation Readme file	2025-11-25 13:05:27 +01:00
Eric Coissac	053d2e28cb	A pretty jupyter login	2025-11-25 13:00:02 +01:00
				`@@ -0,0 +1 @@`
				.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
				`@@ -1 +0,0 @@`
				.admonition{margin:1rem 0;border-radius:4px;box-shadow:0 1px 3px rgba(0,0,0,0.12);transition:all 0.3s ease}.admonition-header{padding:0.5rem 1rem;display:flex;align-items:center;font-weight:600;border-bottom:1px solid rgba(0,0,0,0.1);font-size:1.1rem;border-radius:4px 4px 0 0}.admonition-header svg{width:1.1em;height:1.1em;margin-right:0.5rem;fill:currentColor}.admonition-content{padding:1rem;background-color:#fff;border-radius:0 0 4px 4px;color:#000;transition:background-color 0.3s ease, color 0.3s ease}.admonition-content p{margin:0 0 0.5rem 0}.admonition-content p:last-child{margin-bottom:0}.admonition-content ul,.admonition-content ol{margin:0 0 0.5rem 0;padding-left:1.2rem}.admonition-content ul:last-child,.admonition-content ol:last-child{margin-bottom:0}.admonition-content blockquote{margin:0 0 0.5rem 0;padding-left:1rem;border-left:3px solid #e0e0e0}.admonition-content blockquote:last-child{margin-bottom:0}.admonition-content code{background-color:#f5f5f5;color:#24292e;padding:0.2em 0.4em;border-radius:3px;font-size:0.9em}@media (prefers-color-scheme: dark){.admonition-content{background-color:#1D1E20;color:#e6e6e6}.admonition-content code{background-color:#313244;color:#cdd6f4}.admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}}body.dark .admonition-content{background-color:#1D1E20;color:#e6e6e6}body.dark .admonition-content code{background-color:#313244;color:#cdd6f4}body.dark .admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}.admonition.abstract{background:transparent;border-left:4px solid #209fb5}.admonition.abstract .admonition-header{background:rgba(32,159,181,0.1);color:#209fb5}.admonition.caution{background:transparent;border-left:4px solid #e64553}.admonition.caution .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.code{background:transparent;border-left:4px solid #7287fd}.admonition.code .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.conclusion{background:transparent;border-left:4px solid #dd7878}.admonition.conclusion .admonition-header{background:rgba(221,120,120,0.1);color:#dd7878}.admonition.danger{background:transparent;border-left:4px solid #fe640b}.admonition.danger .admonition-header{background:rgba(254,100,11,0.1);color:#fe640b}.admonition.error{background:transparent;border-left:4px solid #d20f39}.admonition.error .admonition-header{background:rgba(210,15,57,0.1);color:#d20f39}.admonition.example{background:transparent;border-left:4px solid #dc8a78}.admonition.example .admonition-header{background:rgba(220,138,120,0.1);color:#dc8a78}.admonition.experiment{background:transparent;border-left:4px solid #51bb2a}.admonition.experiment .admonition-header{background:rgba(81,187,42,0.1);color:#51bb2a}.admonition.goal{background:transparent;border-left:4px solid #e64553}.admonition.goal .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.idea{background:transparent;border-left:4px solid #df8e1d}.admonition.idea .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}.admonition.important{background:transparent;border-left:4px solid #7D4DDA}.admonition.important .admonition-header{background:rgba(125,77,218,0.1);color:#7D4DDA}.admonition.info{background:transparent;border-left:4px solid #04a5e5}.admonition.info .admonition-header{background:rgba(4,165,229,0.1);color:#04a5e5}.admonition.memo{background:transparent;border-left:4px solid #e64553}.admonition.memo .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.note{background:transparent;border-left:4px solid #096ae1}.admonition.note .admonition-header{background:rgba(9,106,225,0.1);color:#096ae1}.admonition.notify{background:transparent;border-left:4px solid #0d48bd}.admonition.notify .admonition-header{background:rgba(13,72,189,0.1);color:#0d48bd}.admonition.question{background:transparent;border-left:4px solid #179299}.admonition.question .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.quote{background:transparent;border-left:4px solid #7287fd}.admonition.quote .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.success{background:transparent;border-left:4px solid #40a02b}.admonition.success .admonition-header{background:rgba(64,160,43,0.1);color:#40a02b}.admonition.task{background:transparent;border-left:4px solid #8839ef}.admonition.task .admonition-header{background:rgba(136,57,239,0.1);color:#8839ef}.admonition.tip{background:transparent;border-left:4px solid #179299}.admonition.tip .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.warning{background:transparent;border-left:4px solid #df8e1d}.admonition.warning .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}