A pretty jupyter login

Make cleaning
Add pedagogic content
2025-11-21 14:40:46 +01:00 · 2025-11-17 14:18:13 +01:00 · 2025-11-16 14:55:30 +01:00 · 2025-11-16 14:55:30 +01:00 · 2025-11-05 17:28:55 +01:00 · 2025-10-31 19:56:10 +01:00
437 changed files with 1256224 additions and 304 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,15 @@
+/Affinity
+/jupyterhub_volumes/users
+/jupyterhub_volumes/shared
+/jupyterhub_volumes/jupyterhub
+/jupyterhub_volumes/caddy
+/jupyterhub_volumes/course/data/Genbank
+/**/.DS_Store
+/web_src/**/*.RData
+/web_src/**/*.pdf
+/web_src/**/*_files
+/web_src/**/*_cache
+/.luarc.json
+/sandbox
+*.log
+ncbitaxo_*
--- a/.vscode/ltex.hiddenFalsePositives.en-US.txt
+++ b/.vscode/ltex.hiddenFalsePositives.en-US.txt
@@ -0,0 +1 @@
+{"rule":"MORFOLOGIK_RULE_EN_US","sentence":"^\\QA password that secures access to the system\nA user number or UID (User IDentifier) that identifies the user on the machine\nA location on the hard disk to store the user's files, called Home or home\nA group of users, which allows working in groups on the machine (see later)\\E$"}
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "git.enabled": false
+}
--- a/49
+++ b/49
@@ -1,49 +0,0 @@
-# ---------- Stage 1 : builder ----------
-FROM jupyter/base-notebook:latest AS builder
-
-USER root
-
-# Install system dependencies for R, build tools and Go/Rust
-RUN apt-get update && apt-get install -y \
-    r-base r-base-dev \
-    libcurl4-openssl-dev libssl-dev libxml2-dev \
-    build-essential git curl \
-    && apt-get clean && rm -rf /var/lib/apt/lists/*
-
-# Install R kernel + useful packages
-RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
-    R -e "IRkernel::installspec(user = FALSE)" && \
-    R -e "install.packages(c('tidyverse','vegan','ade4'), repos='http://cran.rstudio.com/')"
-
-# Install bash kernel
-RUN pip install bash_kernel && python -m bash_kernel.install --sys-prefix
-
-# Install obitools4
-RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
-
-# Install csvkit
-RUN pip install csvkit
-
-# Install csvlens via Rust
-RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
-    . $HOME/.cargo/env && \
-    cargo install csvlens
-
-RUN apt-get update && apt-get install -y ruby ruby-dev build-essential \
-    && gem install youplot
-
-# Copy csvlens to /usr/local/bin for final use
-RUN cp $HOME/.cargo/bin/csvlens /usr/local/bin/
-
-# Set permissions for Jupyter user
-RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
-    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER} 
-
-# Switch back to Jupyter user
-USER ${NB_UID}:${NB_GID}
-WORKDIR /home/${NB_USER}/work
-
-# Environment variables
-ENV PATH="/home/${NB_USER}/work/course/bin:${PATH}"
-ENV R_LIBS_USER="/home/${NB_USER}/work/R_packages"
-ENV R_LIBS_SITE="/home/${NB_USER}/work/course/R_packages:/usr/local/lib/R/site-library:/usr/lib/R/site-library"
--- a/Readme.md
+++ b/Readme.md
@@ -1,96 +1,127 @@
 # JupyterHub Configuration with OrbStack on Mac (all in Docker)

 ## Prerequisites
- OrbStack installed and running

-## File Structure
+You must have docker running on your computer

-Your `~/jupyterhub-tp` directory should contain:
-```
-~/jupyterhub-tp/
-├── Dockerfile                  # Image for students (already created)
-├── Dockerfile.hub              # Image for JupyterHub (new)
-├── jupyterhub_config.py        # Configuration
-├── docker-compose.yml          # Orchestration
-└── start-jupyterhub.sh         # Startup script
-```
+-   On MacOS, [OrbStack](https://orbstack.dev/ "A Docker implementation optimised for MacOS") is recommanded

 ## Installation Steps

 ### 1. Create Directory Structure

 ```bash
-mkdir -p ~/jupyterhub-tp
-cd ~/jupyterhub-tp
+git clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git
 ```

-### 2. Create All Necessary Files
-
-Create the following files with the content from artifacts:
- `Dockerfile` (artifact "Dockerfile for JupyterHub with R and Bash")
- `Dockerfile.hub` (artifact "Dockerfile for JupyterHub container")
- `jupyterhub_config.py` (artifact "JupyterHub Configuration")
- `docker-compose.yml` (artifact "docker-compose.yml")
- `start-jupyterhub.sh` (artifact "start-jupyterhub.sh")
-
-### 3. Make Startup Script Executable
+Enter into the `OBIJupyterHub` directory

 ```bash
-chmod +x start-jupyterhub.sh
+cd OBIJupyterHub
 ```

-### 4. Start JupyterHub
+#### File Structure

-```bash
+Your `OBIJupyterHub` directory should contain:
+
+```         
+OBIJupyterHub
+├── start-jupyterhub.sh                  - The script used to setup and start the server
+├── obijupyterhub                        - The files describing the docker images and the stack
+│   ├── Caddyfile
+│   ├── 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
+```
+
+### 2. Start JupyterHub
+
+From the terminal, in the `OBIJupyterHub` directory, run the following command:
+
+``` bash
 ./start-jupyterhub.sh
 ```

-### 5. Access JupyterHub
+### 3. Access JupyterHub

 Open your browser and go to: **http://localhost:8888**

-You can log in with any username and password: `metabar2025`
+You can log in as a student with any username and password: `metabar2025`

 ## Useful Commands

 ### View JupyterHub logs
-```bash
+
+``` bash
+cd obijupyterhub
 docker-compose logs -f jupyterhub
 ```

 ### View all containers (hub + students)
-```bash
-docker ps
+
+``` bash
+docker ps | grep jupyterhub
 ```

 ### Stop JupyterHub
-```bash
+
+``` bash
+cd obijupyterhub
 docker-compose down
 ```

 ### Restart JupyterHub (after config modification)
-```bash
-docker-compose restart jupyterhub
-```

-### Rebuild after Dockerfile modification
-```bash
-# For student image
-docker build -t jupyterhub-student:latest -f Dockerfile .
+``` bash
+cd obijupyterhub
 docker-compose restart jupyterhub
-
-# For hub image
-docker-compose up -d --build
 ```

 ### View logs for a specific student
-```bash
-docker logs jupyter-username
+
+``` bash
+docker logs jupyter-<username>
 ```

+Replace `<username>` by the actual username of the student.
+
 ### Clean up after lab
-```bash
+
+``` bash
 # Stop and remove all containers
+cd obijupyterhub
 docker-compose down

 # Remove student containers
@@ -110,8 +141,9 @@ docker volume prune -f
 ### Directory Structure for Each Student

 Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):
-```
-work/                              # Personal workspace root (persistent)
+
+```         
+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)
@@ -121,56 +153,38 @@ work/                              # Personal workspace root (persistent)
    └── [course materials]        # Your course files
 ```

-**R Package Priority:**
-1. R checks `work/R_packages/` first (personal, writable)
-2. Then `work/course/R_packages/` (shared, read-only, installed by prof)
-3. Then system libraries
+**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.

 ### User Accounts

-**Admin Account:**
- Username: `admin`
- Password: `admin2025` (change in docker-compose.yml: `JUPYTERHUB_ADMIN_PASSWORD`)
+**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`)
+**Student Accounts:** 
+
+- Username: any name 
+- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`) 
 - Read-only access to `course/` directory

 ### Installing R Packages (Admin Only)

 **From your Mac (recommended):**

-```bash
-chmod +x install-r-packages-admin.sh
-
+``` bash
 # Install packages
-./install-r-packages-admin.sh reshape2 plotly knitr
+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
-
-**From admin notebook:**
-
-Login as `admin` and create an R notebook:
-
-```r
-# Install packages in course/R_packages (admin only, available to all students)
-course_lib <- "/home/jovyan/work/course/R_packages"
-dir.create(course_lib, recursive = TRUE, showWarnings = FALSE)
-
-install.packages(c('reshape2', 'plotly', 'knitr'), 
-                 lib = course_lib,
-                 repos = 'http://cran.rstudio.com/')
-```
-
-Note: Admin account has write access to the course directory.
+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:**

@@ -178,25 +192,27 @@ Students can install packages in their personal `work/R_packages/`:

 ```r
 # Install in personal library (each student has their own)
-install.packages(c('mypackage'))  # Will install in work/R_packages/
+install.packages('mypackage')  # Will install in work/R_packages/
 ```

 ### Using R Packages (Students)

 Students simply load packages normally:
-```r
+
+``` r
 library(reshape2)  # R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system
 library(plotly)
 ```

-R automatically searches in this order:
-1. Personal packages: `/home/jovyan/work/R_packages/` (R_LIBS_USER)
-2. Prof packages: `/home/jovyan/work/course/R_packages/` (R_LIBS_SITE)
-3. System packages
+R automatically searches in this order: 
+
+1. Personal packages: `/home/jovyan/work/R_packages/` (R_LIBS_USER) 
+1. Prof packages: `/home/jovyan/work/course/R_packages/` (R_LIBS_SITE) 
+1. System packages

 ### List Available Packages

-```r
+``` r
 # List all available packages (personal + course + system)
 installed.packages()[,"Package"]

@@ -211,7 +227,7 @@ list.files("/home/jovyan/work/course/R_packages")

 To put files in the `course/` directory (accessible read-only):

-```bash
+``` bash
 # Create a temporary directory
 mkdir -p ~/jupyterhub-tp/course-files

@@ -226,34 +242,21 @@ docker run --rm \
  alpine sh -c "cp -r /source/* /target/"
 ```

-### Access Shared Files Between Students
-
-Students can collaborate via the `shared/` directory:
-
-```python
-# In a notebook, to read a shared file
-import pandas as pd
-df = pd.read_csv('/home/jovyan/work/shared/group_data.csv')
-
-# To write a shared file
-df.to_csv('/home/jovyan/work/shared/alice_results.csv')
-```
-
 ### Retrieve Student Work

-```bash
+``` bash
 # List user volumes
-docker volume ls | grep jupyterhub-user
+docker volume ls | grep 'obijupyterhub_user-'

 # Copy files from a specific student
 docker run --rm \
-  -v jupyterhub-user-alice:/source \
+  -v obijupyterhub_user-alice:/source \
  -v ~/submissions:/target \
  alpine sh -c "cp -r /source/* /target/alice/"

 # Copy all shared work
 docker run --rm \
-  -v jupyterhub-shared:/source \
+  -v obijupyterhub_shared:/source \
  -v ~/submissions/shared:/target \
  alpine sh -c "cp -r /source/* /target/"
 ```
@@ -261,14 +264,18 @@ docker run --rm \
 ## User Management

 ### Option 1: Predefined User List
+
 In `jupyterhub_config.py`, uncomment and modify:
-```python
+
+``` python
 c.Authenticator.allowed_users = {'student1', 'student2', 'student3'}
 ```

 ### Option 2: Allow Everyone (for testing)
+
 By default, the configuration allows any user:
-```python
+
+``` python
 c.Authenticator.allow_all = True
 ```

@@ -276,75 +283,87 @@ c.Authenticator.allow_all = True

 ## Kernel Verification

-Once logged in, create a new notebook and verify you have access to:
- **Python 3** (default kernel)
- **R** (R kernel)
+Once logged in, create a new notebook and verify you have access to: 
+
+- **Python 3** (default kernel) 
+- **R** (R kernel) 
 - **Bash** (bash kernel)

 ## Customization for Your Labs

 ### Add Additional R Packages
+
 Modify the `Dockerfile` (before `USER ${NB_UID}`):
-```dockerfile
+
+``` dockerfile
 RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
 ```

-Then rebuild:
+Then restart the server (it rebuilds the images if needed):
+
 ```bash
-docker build -t jupyterhub-student:latest -f Dockerfile .
-docker-compose restart jupyterhub
+./start-jupyterhub.sh
 ```

 ### Add Python Packages
+
 Add to the `Dockerfile` (before `USER ${NB_UID}`):
-```dockerfile
+
+``` dockerfile
 RUN pip install numpy pandas matplotlib seaborn
 ```

 ### Distribute Files to Students
+
 Create a `files_lab/` directory and add to the `Dockerfile`:
-```dockerfile
+
+``` dockerfile
 COPY files_lab/ /home/${NB_USER}/lab/
 RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
 ```

 ### Change Port (if 8000 is occupied)
+
 Modify in `docker-compose.yml`:
-```yaml
+
+``` yaml
 ports:
  - "8001:8000"  # Accessible on localhost:8001
 ```

 ## Advantages of This Approach

-✅ **Everything in Docker**: No need to install Python/JupyterHub on your Mac  
-✅ **Portable**: Easy to deploy on another Mac or server  
-✅ **Isolated**: No pollution of your system environment  
-✅ **Easy to Clean**: A simple `docker-compose down` is enough  
+✅ **Everything in Docker**: No need to install Python/JupyterHub on your computer\
+✅ **Portable**: Easy to deploy on another server\
+✅ **Isolated**: No pollution of your system environment\
+✅ **Easy to Clean**: A simple `docker-compose down` is enough\
 ✅ **Reproducible**: Students will have exactly the same environment

 ## Troubleshooting

-**Error "Cannot connect to Docker daemon"**:
- Check that OrbStack is running
+**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`
+**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**:
+**Port 8000 already in use**: 
+
 - Change port in `docker-compose.yml`

-**After config modification, changes are not applied**:
-```bash
-docker-compose restart jupyterhub
-```

 **I want to start from scratch**:
-```bash
+
+``` bash
+push obijupyterhub
 docker-compose down -v
 docker rmi jupyterhub-hub jupyterhub-student
+popd
+
 # Then rebuild everything
 ./start-jupyterhub.sh
-```
+```
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,37 +0,0 @@
-services:
-  jupyterhub:
-    build:
-      context: .
-      dockerfile: Dockerfile.hub
-    container_name: jupyterhub
-    image: jupyterhub-hub:latest
-    ports:
-      - "8888:8000"
-    volumes:
-      # Access to Docker socket to spawn student containers
-      - /var/run/docker.sock:/var/run/docker.sock
-      # JupyterHub database persistence
-      - jupyterhub-data:/srv/jupyterhub
-      # Mount config file directly (for easy modifications)
-      - ./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
-    networks:
-      - jupyterhub-network
-    restart: unless-stopped
-    environment:
-      # Shared password for all students
-      JUPYTERHUB_PASSWORD: metabar2025
-      # Admin password (for installing R packages)
-      JUPYTERHUB_ADMIN_PASSWORD: admin2025
-      # Optional environment variables
-      DOCKER_NOTEBOOK_DIR: /home/jovyan/work
-
-networks:
-  jupyterhub-network:
-    name: jupyterhub-network
-    driver: bridge
-
-volumes:
-  jupyterhub-data:
-  jupyterhub-shared:
-  jupyterhub-course:
-  
--- a/fish-primers.qmd
+++ b/fish-primers.qmd
@@ -0,0 +1,862 @@
+---
+title: "Designing Fish primers"
+format: revealjs
+editor: visual
+---
+
+```{r setup, include=FALSE}
+library(knitr)
+```
+
+# Preparing the data
+
+------------------------------------------------------------------------
+
+## What do we need ?
+
+To design a new animal DNA metabarcode we download from the NCBI the following data
+
+-   The complete set of whole mitochondrial genomes
+-   The NCBI taxonomy
+
+------------------------------------------------------------------------
+
+## We need also:
+
+-   a Unix computer: a Mac or a Linux box
+-   A unix terminal window for typing commands
+-   Installed on the computer
+    -   The OBITools --- <http://github.com/metabarcoding/obitools4>
+    -   ecoPrimers --- <http://metabarcoding.org/ecoprimers>
+    -   R --- <http://wwww.r-project.org>
+
+------------------------------------------------------------------------
+
+## Downloading the mitochondrial genomes
+
+We can use an internet browser and download the files from NCBI FTP website
+
+![](ncbi-ftp.png){fig-align="center"}
+
+------------------------------------------------------------------------
+
+## Downloading the mitochondrial genomes
+
+We can use an internet browser and download the files from NCBI FTP website
+
+or run the following command lines
+
+```{bash}
+#| eval: false
+#| echo: true
+curl 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/mitochondrion/mitochondrion.1.genomic.gbff.gz' \
+     > mito.all.gb.gz
+```
+
+------------------------------------------------------------------------
+
+```{bash}
+#| eval: false
+#| echo: true
+zless mito.all.gb.gz
+```
+
+```         
+LOCUS       NW_009243181           45189 bp    DNA     linear   CON 06-OCT-2014
+DEFINITION  Fonticula alba strain ATCC 38817 mitochondrial scaffold
+            supercont2.211, whole genome shotgun sequence.
+ACCESSION   NW_009243181 NZ_AROH01000000
+VERSION     NW_009243181.1
+DBLINK      BioProject: PRJNA262900
+            Assembly: GCF_000388065.1
+KEYWORDS    WGS; RefSeq.
+SOURCE      mitochondrion Fonticula alba
+  ORGANISM  Fonticula alba
+            Eukaryota; Rotosphaerida; Fonticulaceae; Fonticula.
+REFERENCE   1  (bases 1 to 45189)
+```
+
+------------------------------------------------------------------------
+
+## Downloading the complete taxonomy
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy --download-ncbi
+```
+
+```         
+INFO[0000] Number of workers set 16                     
+INFO[0000] Downloading NCBI Taxdump to ncbitaxo_20250211.tgz 
+downloading 100% ████████████████████████████████████████| (66/66 MB, 5.1 MB/s)   
+```
+
+The NCBI taxonomy contains all the relationship between taxa. Each taxon is identified by a unique numerical id: `taxid`
+
+------------------------------------------------------------------------
+
+## The archive contains several files
+
+file: `nodes.dmp`
+
+```         
+1  |  1  |  no rank  |      |   8   |   0   | ...
+2   |   131567  |   superkingdom    |       |   0   |   0   |
+6   |   335928  |   genus   |       |   0   |   1   |
+7   |   6   |   species |   AC  |   0   |   1   |
+9   |   32199   |   species |   BA  |   0   |
+10  |   135621  |   genus   |       |   0   |
+11  |   1707    |   species |   CG  |   0   |   1   |
+13  |   203488  |   genus   |       |   0   |   1   |
+14  |   13  |   species |   DT  |   0   |   1   |
+```
+
+------------------------------------------------------------------------
+
+## file: `names.dmp`
+
+```         
+1   |   root    |       |   scientific name |
+2   |   Bacteria    |   Bacteria <prokaryote>   |   scientific name |
+2   |   Monera  |   Monera <Bacteria>   |   in-part |
+2   |   Procaryotae |   Procaryotae <Bacteria>  |   in-part |
+2   |   Prokaryota  |   Prokaryota <Bacteria>   |   in-part |
+2   |   Prokaryotae |   Prokaryotae <Bacteria>  |   in-part |
+2   |   bacteria    |   bacteria <blast2>   |   blast name  |
+2   |   eubacteria  |       |   genbank common name |
+2   |   prokaryote  |   prokaryote <Bacteria>   |   in-part |
+...
+10  |   Cellvibrio  |       |   scientific name |
+11  |   [Cellvibrio] gilvus |       |   scientific name |
+13  |   Dictyoglomus    |       |   scientific name |
+14  |   Dictyoglomus thermophilum   |       |   scientific name |
+```
+
+------------------------------------------------------------------------
+
+## Preparing the set of complete genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+obiconvert --skip-empty \
+           --update-taxid \
+           -t ncbitaxo_20250211.tgz \
+           mito.all.gb.gz \
+       > mito.all.fasta
+head -5 mito.all.fasta
+```
+
+five first lines of the new `mito.all.fasta` file
+
+```         
+>NC_072933 {"definition":"Echinosophora koreensis mitochondrion, complete genome.","scientific_name":"mitochondrion Echinosophora koreensis","taxid":228658}
+ctttcgggtcggaaatagaagatctggattagatcccttctcgatagctttagtcagagc
+tcatccctcgaaaaagggagtagtgagatgagaaaagggtgactagaatacggaaattca
+actagtgaagtcagatccgggaattccactattgaagttatccgtcttaggcttcaagca
+agctatctttcaaggaagtcagtctaagccctaagccaagatctgctttttgccagtcaa
+```
+
+------------------------------------------------------------------------
+
+## We want:
+
+-   annotate sequences by their species `taxid`
+-   keep a single genome per species
+-   extract only vertebrate genome
+
+------------------------------------------------------------------------
+
+## Looking for the **Vertebrata**'s taxid
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'vertebrata'
+```
+
+``` csv
+taxid,parent,taxonomic_rank,scientific_name
+taxon:1261581 [Vertebrata]@genus,taxon:2008651 [Polysiphonioideae]@subfamily,genus,Vertebrata
+taxon:7742 [Vertebrata]@clade,taxon:89593 [Craniata]@subphylum,clade,Vertebrata
+```
+
+------------------------------------------------------------------------
+
+## Looking for the **Vertebrata**'s taxid
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'vertebrata' \
+    | csvlook
+```
+
+``` csv
+| taxid                            | parent                                      | taxonomic_rank | scientific_name |
+| -------------------------------- | ------------------------------------------- | -------------- | --------------- |
+| taxon:1261581 [Vertebrata]@genus | taxon:2008651 [Polysiphonioideae]@subfamily | genus          | Vertebrata      |
+| taxon:7742 [Vertebrata]@clade    | taxon:89593 [Craniata]@subphylum            | clade          | Vertebrata      |
+```
+
+## A genus called **Vertebrata**
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              -p 2008651 \
+      | csvlook
+```
+
+``` csv
+| taxid                                       | parent                                      | taxonomic_rank | scientific_name    |
+| ------------------------------------------- | ------------------------------------------- | -------------- | ------------------ |
+| taxon:2008651 [Polysiphonioideae]@subfamily | taxon:2803 [Rhodomelaceae]@family           | subfamily      | Polysiphonioideae  |
+| taxon:2803 [Rhodomelaceae]@family           | taxon:2802 [Ceramiales]@order               | family         | Rhodomelaceae      |
+| taxon:2802 [Ceramiales]@order               | taxon:2045261 [Rhodymeniophycidae]@subclass | order          | Ceramiales         |
+| taxon:2045261 [Rhodymeniophycidae]@subclass | taxon:2806 [Florideophyceae]@class          | subclass       | Rhodymeniophycidae |
+| taxon:2806 [Florideophyceae]@class          | taxon:2763 [Rhodophyta]@phylum              | class          | Florideophyceae    |
+| taxon:2763 [Rhodophyta]@phylum              | taxon:2759 [Eukaryota]@superkingdom         | phylum         | Rhodophyta         |
+| taxon:2759 [Eukaryota]@superkingdom         | taxon:131567 [cellular organisms]@no rank   | superkingdom   | Eukaryota          |
+| taxon:131567 [cellular organisms]@no rank   | taxon:1 [root]@no rank                      | no rank        | cellular organisms |
+| taxon:1 [root]@no rank                      | taxon:1 [root]@no rank                      | no rank        | root               |
+```
+
+------------------------------------------------------------------------
+
+## Reannotation and selection of the genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+obiannotate -t ncbitaxo_20250211.tgz \
+            --with-taxon-at-rank=species \
+            mito.all.fasta | \
+  obiannotate -S 'ori_taxid=annotations.taxid' | \
+  obiannotate -S 'taxid=annotations.species_taxid' | \
+  obiuniq -c taxid > mito.one.fasta
+```
+
+------------------------------------------------------------------------
+
+## Species representation
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obicsv -k taxid mito.one.fasta \
+     | tail -n +2 \
+     | sort \
+     | uniq -c \
+     | sort -nk1 \
+     | cut -w -f 2 \
+     | uplot count
+```
+
+```         
+     ┌                                        ┐ 
+   1 ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 17769.0   
+   2 ┤ 90.0                                     
+   3 ┤ 17.0                                     
+   4 ┤ 5.0                                      
+   5 ┤ 4.0                                      
+   6 ┤ 2.0                                      
+   7 ┤ 1.0                                      
+     └                                        ┘ 
+```
+
+------------------------------------------------------------------------
+
+## Selection of the vertebrata genomes
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obigrep -t ncbitaxo_20250211.tgz \
+        -r 7742 \
+        mito.one.fasta > mito.vert.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+
+obicount mito.vert.fasta \
+   | csvlook
+```
+
+```         
+| entities |           n |
+| -------- | ----------- |
+| variants |       7,822 |
+| reads    |       7,823 |
+| symbols  | 131,378,756 |
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 1/3
+
+```{bash}
+#| eval: false
+#| echo: true
+mkdir ncbitaxo_20250211
+cd ncbitaxo_20250211
+tar zxvf ../ncbitaxo_20250211.tgz 
+cd ..
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 2/3
+
+```{bash}
+#| eval: false
+#| echo: true
+obiconvert -O mito.vert.fasta > mito.vert.old.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+head -5 mito.vert.old.fasta
+```
+
+``` csv
+>NC_071784 taxid=taxon:2065826 [Sineleotris saccharae]@species; count=1; ori_taxid=taxon:2065826 [Sineleotris saccharae]@species; scientific_name=mitochondrion Sineleotris saccharae; species_name=Sineleotris saccharae; species_taxid=taxon:2065826 [Sineleotris saccharae]@species;  Sineleotris saccharae mitochondrion, complete genome.
+gctagcgtagcttaaccaaagcataacactgaagatgttaagatgggccctagaaagccc
+cgcaagcacaaaagcttggtcctggctttactatcagcttaggctaaacttacacatgca
+agtatccgcatccccgtgagaatgcccttaagctcccaccgctaacaggagtcaaggagc
+cggtatcaggcacaaccctgagttagcccacgacaccttgctcagccacacccccaaggg
+```
+
+------------------------------------------------------------------------
+
+## Prepare data for ecoPrimers 3/3
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPCRFormat -t ncbitaxo_20250211 \
+             -f \
+             -n vertebrata \
+             mito.vert.old.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+ls -l vertebrata*
+```
+
+```         
+-rw-r--r--@ 1 coissac  staff  260899785 Feb 11 11:53 vertabrata.ndx
+-rw-r--r--@ 1 coissac  staff        546 Feb 11 11:53 vertabrata.rdx
+-rw-r--r--@ 1 coissac  staff  121379751 Feb 11 11:53 vertabrata.tdx
+-rw-r--r--@ 1 coissac  staff   40446318 Feb 11 11:54 vertabrata_001.sdx
+```
+
+------------------------------------------------------------------------
+
+## Looking for the *Teleostei* `taxid`
+
+```{bash}
+#| eval: false
+#| echo: true
+obitaxonomy -t ncbitaxo_20250211.tgz \
+              --fixed \
+              'Teleostei' \
+    | csvlook
+```
+
+``` csv
+| taxid                              | parent                             | taxonomic_rank | scientific_name |
+| ---------------------------------- | ---------------------------------- | -------------- | --------------- |
+| taxon:32443 [Teleostei]@infraclass | taxon:41665 [Neopterygii]@subclass | infraclass     | Teleostei       |
+```
+
+------------------------------------------------------------------------
+
+## Selecting the best primer pairs
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPrimers -d vertebrata \
+           -e 3 -3 2 \
+           -l 30 -L 150 \
+           -r 32443 \
+           -c > Teleostei.ecoprimers
+```
+
+-   Total pair count : 9407
+-   Total good pair count : 407
+
+------------------------------------------------------------------------
+
+```{bash}
+#| eval: false
+#| echo: true
+head -35 Teleostei.ecoprimers
+```
+
+``` csv
+#
+# ecoPrimer version 0.5
+# Rank level optimisation : species
+# max error count by oligonucleotide : 3
+#
+# Restricted to taxon:
+#     32443 : Teleostei (infraclass)
+#
+# strict primer quorum  : 0.70
+# example quorum        : 0.90
+# counterexample quorum : 0.10
+#
+# database : vertebrata
+# Database is constituted of  3909 examples        corresponding to  3876 species
+#                        and     0 counterexamples corresponding to     0 species
+#
+# amplifiat length between [30,150] bp
+# DB sequences are considered as circular
+# Pairs having specificity less than 0.60 will be ignored
+#
+     0  AGAGTGACGGGCGGTGTG      CGTCAGGTCGAGGTGTAG      62.8    42.4    57.5    34.1    12      11      GG      3864    0       0.988   3832    0       0.989   2731    0.713      134     146     138.22
+     1  CGTCAGGTCGAGGTGTAG      GAGTGACGGGCGGTGTGT      57.5    34.1    63.1    42.9    11      12      GG      3863    0       0.988   3831    0       0.988   2730    0.713      133     145     137.22
+     2  CGTCAGGTCGAGGTGTAG      GGGAGAGTGACGGGCGGT      57.5    34.1    64.5    37.0    11      13      GG      3811    0       0.975   3779    0       0.975   2689    0.712      137     149     141.22
+     3  CGTCAGGTCGAGGTGTAG      GGGGAGAGTGACGGGCGG      57.5    34.1    65.5    38.4    11      14      GG      3804    0       0.973   3772    0       0.973   2682    0.711      138     149     142.22
+     4  ACACCGCCCGTCACTCTC      ACCTTCCGGTACACTTAC      62.5    36.8    54.0    16.6    12      9       GG      3850    0       0.985   3818    0       0.985   2658    0.696      46      132     66.51
+     5  AACGTCAGGTCGAGGTGT      AGAGTGACGGGCGGTGTG      58.8    28.4    62.8    41.7    10      12      GG      3779    0       0.967   3746    0       0.966   2653    0.708      137     148     140.23
+     6  ACACCGCCCGTCACTCTC      CACCTTCCGGTACACTTA      62.5    36.8    54.0    16.6    12      9       GG      3846    0       0.984   3814    0       0.984   2654    0.696      47      133     67.51
+     7  AACGTCAGGTCGAGGTGT      GAGTGACGGGCGGTGTGT      58.8    28.4    63.1    42.1    10      12      GG      3778    0       0.966   3745    0       0.966   2652    0.708      136     147     139.23
+     8  ACCTTCCGGTACACTTAC      CACACCGCCCGTCACTCT      54.0    16.6    62.8    37.3    9       12      GG      3845    0       0.984   3813    0       0.984   2653    0.696      47      133     67.51
+     9  ACACCGCCCGTCACTCTC      TCCGGTACACTTACCATG      62.5    36.8    54.1    18.1    12      9       GG      3851    0       0.985   3819    0       0.985   2651    0.694      42      128     62.51
+    10  ACACCGCCCGTCACTCTC      CCGGTACACTTACCATGT      62.5    36.8    54.4    18.6    12      9       GG      3851    0       0.985   3819    0       0.985   2651    0.694      41      127     61.51
+    11  ACACCGCCCGTCACTCTC      CCAAGTGCACCTTCCGGT      62.5    36.8    60.7    28.9    12      11      GG      3837    0       0.982   3805    0       0.982   2650    0.696      54      140     74.51
+    12  ACACCGCCCGTCACTCTC      GCACCTTCCGGTACACTT      62.5    36.8    57.7    22.5    12      10      GG      3842    0       0.983   3810    0       0.983   2650    0.696      48      134     68.51
+    13  ACACCGCCCGTCACTCTC      CGGTACACTTACCATGTT      62.5    36.8    52.4    15.7    12      8       GG      3850    0       0.985   3818    0       0.985   2650    0.694      40      126     60.51
+    14  ACACCGCCCGTCACTCTC      CACTTACCATGTTACGAC      62.5    36.8    51.1    27.7    12      8       GG      3850    0       0.985   3817    0       0.985   2649    0.694      35      121     55.51
+```
+
+------------------------------------------------------------------------
+
+-   Primer ID : 11
+
+ 
+
+| Primer  | sequence           | tm max | tm min | GC count |
+|---------|--------------------|--------|--------|----------|
+| Forward | ACACCGCCCGTCACTCTC | 62.5   | 36.8   | 12       |
+| Reverse | CCAAGTGCACCTTCCGGT | 60.7   | 28.9   | 11       |
+
+ 
+
+-   amplifying 3837/3909 sequences\
+-   identify 2650/3876 Species
+-   Size ranging from 54bp to 140bp (mean: 74.75 bp)
+
+## Testing the new primer pair
+
+```{bash}
+#| eval: false
+#| echo: true
+obipcr --forward ACACCGCCCGTCACTCTC \
+       --reverse CCAAGTGCACCTTCCGGT \
+       -e 5 \
+       -l 30 -L 150 \
+       -c \
+       mito.vert.fasta \
+       > Teleostei_11.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+head Teleostei_11.fasta
+```
+
+``` csv
+>NC_022183_sub[925..998] {"count":1,"definition":"Acrossocheilus hemispinus mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcaccctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Acrossocheilus hemispinus","species_name":"Acrossocheilus hemispinus","species_taxid":"taxon:356810 [Acrossocheilus hemispinus]@species","taxid":"taxon:356810 [Acrossocheilus hemispinus]@species"}
+cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgt
+aacatggtaagtgt
+>NC_018560_sub[916..988] {"count":1,"definition":"Astatotilapia calliptera mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:8154 [Astatotilapia calliptera]@species","reverse_error":1,"reverse_match":"ccaagtacaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Astatotilapia calliptera (eastern happy)","species_name":"Astatotilapia calliptera","species_taxid":"taxon:8154 [Astatotilapia calliptera]@species","taxid":"taxon:8154 [Astatotilapia calliptera]@species"}
+cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgta
+acatggtaagtgt
+>NC_056117_sub[923..997] {"count":1,"definition":"Pseudocrossocheilus tridentis mitochondrion, complete genome.","direction":"forward","forward_error":0,"forward_match":"acaccgcccgtcactctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","reverse_error":0,"reverse_match":"ccaagtgcaccttccggt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Pseudocrossocheilus tridentis","species_name":"Pseudocrossocheilus tridentis","species_taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species","taxid":"taxon:887881 [Pseudocrossocheilus tridentis]@species"}
+ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcg
+taacacggtaagtgt
+>NC_045904_sub[919..997] {"count":1,"definition":"Eospalax fontanierii mitochondrion, complete genome.","direction":"forward","forward_error":1,"forward_match":"acaccgcccgtcgctctc","forward_primer":"ACACCGCCCGTCACTCTC","ori_taxid":"taxon:146134 [Eospalax fontanierii]@species","reverse_error":4,"reverse_match":"ccaagcacactttccagt","reverse_primer":"CCAAGTGCACCTTCCGGT","scientific_name":"mitochondrion Eospalax fontanierii","species_name":"Eospalax fontanierii","species_taxid":"taxon:146134 [Eospalax fontanierii]@species","taxid":"taxon:146134 [Eospalax fontanierii]@species"}
+```
+
+------------------------------------------------------------------------
+
+convert the fasta file to csv
+
+```{bash}
+#| eval: false
+#| echo: true
+obicsv --auto -s -i Teleostei_11.fasta > Teleostei_11.csv
+```
+
+and display the begining of the table
+
+```{bash}
+#| eval: false
+#| echo: true
+head Teleostei_11.csv | csvlook
+```
+
+``` csv
+| id                        | count | direction | forward_error | forward_match      | forward_primer     | ori_taxid                                            | reverse_error | reverse_match      | reverse_primer     | scientific_name                                        | species_name                  | species_taxid                                        | taxid                                                | sequence                                                                        |
+| ------------------------- | ----- | --------- | ------------- | ------------------ | ------------------ | ---------------------------------------------------- | ------------- | ------------------ | ------------------ | ------------------------------------------------------ | ----------------------------- | ---------------------------------------------------- | ---------------------------------------------------- | ------------------------------------------------------------------------------- |
+| NC_022183_sub[925..998]   |  True | forward   |          True | acaccgcccgtcaccctc | ACACCGCCCGTCACTCTC | taxon:356810 [Acrossocheilus hemispinus]@species     |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Acrossocheilus hemispinus                | Acrossocheilus hemispinus     | taxon:356810 [Acrossocheilus hemispinus]@species     | taxon:356810 [Acrossocheilus hemispinus]@species     | cccgtcaaaatacaccaaaaatacttaatacaataacactaacaaggggaggcaagtcgtaacatggtaagtgt      |
+| NC_018560_sub[916..988]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:8154 [Astatotilapia calliptera]@species        |             1 | ccaagtacaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Astatotilapia calliptera (eastern happy) | Astatotilapia calliptera      | taxon:8154 [Astatotilapia calliptera]@species        | taxon:8154 [Astatotilapia calliptera]@species        | cccaagccaacaacatcctataaataatacattttaccggtaaaggggaggcaagtcgtaacatggtaagtgt       |
+| NC_056117_sub[923..997]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:887881 [Pseudocrossocheilus tridentis]@species |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Pseudocrossocheilus tridentis            | Pseudocrossocheilus tridentis | taxon:887881 [Pseudocrossocheilus tridentis]@species | taxon:887881 [Pseudocrossocheilus tridentis]@species | ccctgtcaaaaagcatcaaatatatataataaattagcaatgacaaggggaggcaagtcgtaacacggtaagtgt     |
+| NC_045904_sub[919..997]   |  True | forward   |          True | acaccgcccgtcgctctc | ACACCGCCCGTCACTCTC | taxon:146134 [Eospalax fontanierii]@species          |             4 | ccaagcacactttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Eospalax fontanierii                     | Eospalax fontanierii          | taxon:146134 [Eospalax fontanierii]@species          | taxon:146134 [Eospalax fontanierii]@species          | ctcaagtacataaacttggatatattcttaataacccaacaaaaatattagaggagataagtcgtaacaaggtaagcat |
+| NC_018546_sub[916..987]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:30732 [Oryzias melastigma]@species             |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Oryzias melastigma (Indian medaka)       | Oryzias melastigma            | taxon:30732 [Oryzias melastigma]@species             | taxon:30732 [Oryzias melastigma]@species             | cccgacccattttaaaaattaaataaaagatttcaggaactaaggggaggcaagtcgtaacatggtaagtgt        |
+| NC_044151_sub[922..993]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597641 [Sicyopterus squamosissimus]@species   |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus squamosissimus (cling goby)  | Sicyopterus squamosissimus    | taxon:2597641 [Sicyopterus squamosissimus]@species   | taxon:2597641 [Sicyopterus squamosissimus]@species   | cccaaaacaaacacacacataaataagaaaaaatgaaaataaaggggaggcaagtcgtaacatggtaagtgt        |
+| NC_044152_sub[922..994]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:2597642 [Sicyopterus stiphodonoides]@species   |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Sicyopterus stiphodonoides (cling goby)  | Sicyopterus stiphodonoides    | taxon:2597642 [Sicyopterus stiphodonoides]@species   | taxon:2597642 [Sicyopterus stiphodonoides]@species   | cccaaaacaaacacacacataaataagaaaaaantgaaaataaaggggaggcaagtcgtaacatggtaagtgt       |
+| NC_026976_sub[1453..1531] |  True | forward   |          True | acaccgcccgtcactccc | ACACCGCCCGTCACTCTC | taxon:9545 [Macaca nemestrina]@species               |             1 | ccaagtgcaccttccagt | CCAAGTGCACCTTCCGGT | mitochondrion Macaca nemestrina (pig-tailed macaque)   | Macaca nemestrina             | taxon:9545 [Macaca nemestrina]@species               | taxon:9545 [Macaca nemestrina]@species               | ctcaaatatatttaaggaacatcttaactaaacgccctaatatttatatagaggggataagtcgtaacatggtaagtgt |
+| NC_031553_sub[921..995]   |  True | forward   |         False | acaccgcccgtcactctc | ACACCGCCCGTCACTCTC | taxon:643337 [Puntioplites proctozystron]@species    |             0 | ccaagtgcaccttccggt | CCAAGTGCACCTTCCGGT | mitochondrion Puntioplites proctozystron               | Puntioplites proctozystron    | taxon:643337 [Puntioplites proctozystron]@species    | taxon:643337 [Puntioplites proctozystron]@species    | ccctgtcaaaacgcactaaaaatatctaatacaaaagcaccgacaaggggaggcaagtcgtaacacggtaagtgt     |
+```
+
+# We are now switching to R
+
+------------------------------------------------------------------------
+
+## Preparing our R session
+
+First we have to download the two follong libraries
+
+```{r}
+#| echo: true
+library(tidyverse)
+library(ggpubr)
+library(ROBITools4)
+```
+
+------------------------------------------------------------------------
+
+## Loading the data
+
+```{r}
+#| echo: true
+
+fish <- read_csv('Teleostei_11.csv', show_col_types = FALSE)
+taxo <- read_ncbi_taxdump('ncbitaxo_20250211')
+assign_default_taxonomy(taxo)
+```
+
+------------------------------------------------------------------------
+
+Looking for Teleostei taxid
+
+```{r}
+#| echo: true
+teleo_taxid <- ecofind('Teleostei')
+teleo_taxid
+```
+
+------------------------------------------------------------------------
+
+## Format taxids
+
+```{r}
+#| echo: true
+fish %>% mutate(
+  taxid = as_taxid(
+      as.integer(
+         str_split_fixed(
+            str_split_fixed(
+               taxid,pattern = " ", 
+               n = 2)[,1],
+            ":",
+            2)[,2]))
+   ) %>% 
+  as_tbl_obipcr() %>%
+  mutate(across(taxon(),
+                .names="category",
+                .fn=taxonomy_classifier(Teleostei = 32443))) %>%
+  group_by(category) %>%
+  mutate(weight = taxonomic_weights(taxid,taxo)) %>%
+  ungroup() -> fish
+```
+
+------------------------------------------------------------------------
+
+## The fish tibble
+
+```{r}
+#| echo: true
+head(fish,n = 4)
+```
+
+------------------------------------------------------------------------
+
+## Identifying which sequences belongs fish
+
+```{r}
+#| echo: true
+table(fish$category)
+```
+
+------------------------------------------------------------------------
+
+## Testing the conservation of the priming sites
+
+```{r}
+#| echo: true
+pssm_forward <- pssm(fish$forward_match,
+                    weights = fish$weight,
+                    categories = fish$category)
+
+pssm_reverse <- pssm(fish$reverse_match,
+                    weights = fish$weight,
+                    categories = fish$category) 
+```
+
+```{r}
+#| echo: true
+pssm_forward
+```
+
+------------------------------------------------------------------------
+
+## Rescaling the matrix as Shanon entropy
+
+$$
+H = - \sum_{i \in \{A,C,G,T\}} p_i \times \frac{\log(p_i)}{\log(2)}
+$$
+
+```{r}
+#| echo: true
+pssm_forward <- pssm_scale_shanon(pssm_forward)
+pssm_reverse <- pssm_scale_shanon(pssm_reverse)
+```
+
+------------------------------------------------------------------------
+
+## Display the rescaled matrix
+
+```{r}
+#| echo: true
+pssm_forward
+```
+
+------------------------------------------------------------------------
+
+## The DNA logo of our primer pair
+
+```{r}
+#| echo: true
+flogo <- ggbarcodelogo(pssm_forward) + 
+         xlab("Forward primer") + ylab("Bits")
+rlogo <- ggbarcodelogo(pssm_reverse) + 
+         xlab("Reverse primer") + ylab("Bits")
+
+ggarrange(flogo,rlogo,ncol=2) -> dnaplot
+
+dnaplot
+```
+
+------------------------------------------------------------------------
+
+## How many mismatches ?
+
+```{r}
+#| echo: true
+ggbarcodemistmatch(fish$forward_error,
+                   fish$reverse_error,
+                   otu=fish$species_name,
+                   categories=fish$category) + theme_minimal()
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate taxa ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category == "Teleostei"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus","family","order"),
+                           sequence))
+```
+
+------------------------------------------------------------------------
+
+## How many sequences will provide information at rank ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category == "Teleostei"),
+     discriminant_at_rank(taxid, 
+                  c("species","genus","family","order"),
+                           sequence))
+```
+
+------------------------------------------------------------------------
+
+## Is it the same for *Cyprinidae* ?
+
+```{r}
+#| echo: true
+cyprinidae_taxid <- ecofind('Cyprinidae')
+cyprinidae_taxid
+```
+
+------------------------------------------------------------------------
+
+## Classify according to both categories
+
+```{r}
+#| echo: true
+fish %>% 
+  mutate(across(taxon(),
+                .names="category2",
+                .fn=taxonomy_classifier(Teleostei = 32443,
+                                        Cyprinidae = 7953))) -> fish
+
+table(fish$category2)
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate taxa ?
+
+```{r}
+#| echo: true
+with(fish %>% filter(category2 == "Cyprinidae"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus"),
+                           sequence))
+```
+
+# Go back to unix
+
+## We run ecoPrimers and ecoPCR on the select primer pair
+
+```{bash}
+#| eval: false
+#| echo: true
+ecoPrimers -d vertebrata \
+           -e 3 -3 2 \
+           -l 30 -L 150 \
+           -r 7953 -c > Cyprinidae.ecoprimers
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+obipcr --forward ACGGCGTAAAGGGTGGTT \
+       --reverse TATCTAATCCCAGTTTGT \
+       -e 5 \
+       -l 30 -L 500 \
+       -c \
+       mito.vert.fasta \
+       > Cyprinidae_14.fasta
+```
+
+```{bash}
+#| eval: false
+#| echo: true
+obicsv --auto -s -i  Cyprinidae_14.fasta >  Cyprinidae_14.csv
+```
+
+# Go back to R
+
+```{r}
+cyprinidae <- read_csv('Cyprinidae_14.csv', 
+                       show_col_types = FALSE) %>%
+  mutate(
+  taxid = as_taxid(
+      as.integer(
+         str_split_fixed(
+            str_split_fixed(
+               taxid,pattern = " ", 
+               n = 2)[,1],
+            ":",
+            2)[,2]))
+   ) %>% 
+  as_tbl_obipcr() %>%
+  mutate(across(taxon(),
+                .names="category",
+                .fn=taxonomy_classifier(Teleostei = 32443, 
+                                        Cyprinidae = 7953))) %>%
+  group_by(category) %>%
+  mutate(weight = taxonomic_weights(taxid,taxo)) %>%
+  ungroup()
+```
+
+------------------------------------------------------------------------
+
+## Identifying which sequences belongs fish and *Cyprinidae*
+
+```{r}
+#| echo: true
+table(cyprinidae$category)
+```
+
+------------------------------------------------------------------------
+
+## Looking for conservation
+
+```{r}
+#| echo: true
+pssm_forward <- pssm(cyprinidae$forward_match,
+                    weights = cyprinidae$weight,
+                    categories = cyprinidae$category) %>%
+  pssm_scale_shanon()
+
+pssm_reverse <- pssm(cyprinidae$reverse_match,
+                    weights = cyprinidae$weight,
+                    categories = cyprinidae$category) %>%
+  pssm_scale_shanon()
+```
+
+------------------------------------------------------------------------
+
+## Plot the new DNA logo
+
+```{r}
+flogo <- ggbarcodelogo(pssm_forward) + 
+         xlab("Forward primer") + ylab("Bits")
+rlogo <- ggbarcodelogo(pssm_reverse) + 
+         xlab("Reverse primer") + ylab("Bits")
+
+ggarrange(flogo,rlogo,ncol=2) -> dnaplot
+
+dnaplot
+```
+
+------------------------------------------------------------------------
+
+## How many mismatches ?
+
+```{r}
+#| echo: true
+ggbarcodemistmatch(cyprinidae$forward_error,
+                   cyprinidae$reverse_error,
+                   otu=cyprinidae$species_name,
+                   categories=cyprinidae$category) + theme_minimal()
+```
+
+------------------------------------------------------------------------
+
+## Are we discriminate *Cyprinidae* taxa ?
+
+```{r}
+#| echo: true
+with(cyprinidae %>% filter(category == "Cyprinidae"),
+     discriminated_at_rank(taxid, 
+                  c("species","genus"),
+                           sequence))
+```
--- a/jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
+++ b/jupyterhub_volumes/course/biodiversity_metrics_exercises.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/R_stats.ipynb
+++ b/jupyterhub_volumes/course/data/Wolf_diet/R_stats.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/vert01_ref_db.fasta.gz
+++ b/jupyterhub_volumes/course/data/Wolf_diet/vert01_ref_db.fasta.gz
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf.ipynb
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf.ipynb
--- a/jupyterhub_volumes/course/data/Wolf_diet/wolf.pdf
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf.pdf
--- 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/course/data/Wolf_diet/wolf_data_wolf_diet_ngsfilter.csv
+++ b/jupyterhub_volumes/course/data/Wolf_diet/wolf_data_wolf_diet_ngsfilter.csv
@@ -0,0 +1,8 @@
+@param,matching,strict
+@param,primer_mismatches,2
+@param,indels,false
+experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
--- a/jupyterhub_volumes/course/data/ref_db_raw.fasta
+++ b/jupyterhub_volumes/course/data/ref_db_raw.fasta
--- a/jupyterhub_volumes/course/data/ref_db_raw.fasta.zip
+++ b/jupyterhub_volumes/course/data/ref_db_raw.fasta.zip
--- a/jupyterhub_volumes/course/unix_exercises_bash.ipynb
+++ b/jupyterhub_volumes/course/unix_exercises_bash.ipynb
--- a/jupyterhub_volumes/web/.gitignore
+++ b/jupyterhub_volumes/web/.gitignore
@@ -0,0 +1,3 @@
+/.quarto/
+**/*.quarto_ipynb
+/pages/
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+<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<title>DNA Metabarcoding Learning Server</title>
+<style>
+    body {
+        margin: 0;
+        font-family: sans-serif;
+        display: flex;
+        height: 100vh;
+        overflow: hidden;
+    }
+
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+    nav {
+        width: 250px;
+        background-color: #2c3e50;
+        color: white;
+        display: flex;
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+        padding: 20px 0;
+        overflow-y: auto;
+    }
+
+    nav ul {
+        list-style: none;
+        padding-left: 15px;
+        margin: 0;
+    }
+
+    nav li {
+        margin: 4px 0;
+    }
+
+    nav a {
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+
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+
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+    }
+
+    /* Admin links */
+    nav .admin-links {
+        border-top: 1px solid #34495e;
+        margin-top: 10px;
+        padding-top: 10px;
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+
+    /* Main content */
+    main {
+        flex: 1;
+        display: flex;
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+
+    header img {
+        width: 100%;
+        max-width: 1000px;
+        height: auto;
+        display: block;
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+
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+
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+        width: 8px;
+    }
+    nav::-webkit-scrollbar-thumb {
+        background-color: #34495e;
+        border-radius: 4px;
+    }
+</style>
+</head>
+<body>
+    <nav>
+        <ul id="nav-menu"></ul>
+        <ul class="admin-links">
+            <li><a href="/obidoc/" target="_blank">OBITools 4 Doc</a></li>
+            <li><a href="/jupyter/" target="_blank">JupyterHub</a></li>
+            <li><a href="/sftp/" target="_blank">Data Admin</a></li>
+        </ul>
+    </nav>
+
+    <main>
+        <header>
+            <img src="img/welcome_metabar.webp" alt="Welcome Banner">
+        </header>
+        <iframe id="content-frame" src=""></iframe>
+    </main>
+
+<script>
+const iframe = document.getElementById("content-frame");
+const navMenu = document.getElementById("nav-menu");
+
+/**
+ * Génère récursivement le menu à partir de l'arborescence JSON
+ */
+function buildMenu(items, parent) {
+    items.forEach(item => {
+        const li = document.createElement("li");
+
+        if (item.children) {
+            const folder = document.createElement("div");
+            folder.className = "folder";
+            folder.textContent = item.label;
+
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+
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+            });
+
+            li.appendChild(folder);
+            li.appendChild(subUl);
+            parent.appendChild(li);
+
+            buildMenu(item.children, subUl);
+        } else if (item.file) {
+            const a = document.createElement("a");
+            a.href = "#";
+            a.textContent = item.label;
+            a.addEventListener("click", e => {
+                e.preventDefault();
+                iframe.src = "pages/" + item.file;
+                history.replaceState(null, null, "#" + item.file);
+            });
+            li.appendChild(a);
+            parent.appendChild(li);
+        }
+    });
+}
+
+fetch('pages/pages.json')
+    .then(resp => resp.json())
+    .then(pages => {
+        buildMenu(pages, navMenu);
+
+        // Charger la page par défaut (1ère sans enfants)
+        let defaultPage = null;
+        function findFirstFile(items) {
+            for (const it of items) {
+                if (it.file) return it.file;
+                if (it.children) {
+                    const child = findFirstFile(it.children);
+                    if (child) return child;
+                }
+            }
+            return null;
+        }
+        defaultPage = findFirstFile(pages);
+
+        if (location.hash) {
+            iframe.src = "pages/" + location.hash.substring(1);
+        } else if (defaultPage) {
+            iframe.src = "pages/" + defaultPage;
+        }
+    })
+    .catch(err => {
+        console.error("Erreur chargement pages.json", err);
+        iframe.srcdoc = "<p>Impossible de charger le contenu.</p>";
+    });
+</script>
+</body>
+</html>
--- a/jupyterhub_volumes/web/obidoc/404.html
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+<html lang="en">
+
+  <head>
+    <meta charset="UTF-8">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+<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>
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+  </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>
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+    <description>Recent content in Categories on OBITools4 documentation</description>
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+  <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/">
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+    <title>Commands on OBITools4 documentation</title>
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+    <description>Recent content in Commands on OBITools4 documentation</description>
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+    <title>http://metabar:8888/obidoc/commands/</title>
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--- 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
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+  <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
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+++ b/jupyterhub_volumes/web/obidoc/docs/commands/alignments/index.xml
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+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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+    <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
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+<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>
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--- 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
@@ -0,0 +1,149 @@
+---
+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
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+    <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" />
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+    <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>
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+      <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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,6 @@
+>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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,604 @@
+#!/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
@@ -0,0 +1,11 @@
+<?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
@@ -0,0 +1,103 @@
+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
@@ -0,0 +1,11 @@
+<?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/ncbitaxo.tgz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/ncbitaxo.tgz
--- 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.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf.fastq
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled.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
@@ -0,0 +1,26 @@
+>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.fastq
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned.fastq
--- 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_assigned_uniq.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_assigned_uniq.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
@@ -0,0 +1,24 @@
+>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
@@ -0,0 +1,329 @@
+>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
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--- 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
@@ -0,0 +1,24 @@
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--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
@@ -0,0 +1,24 @@
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+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
@@ -0,0 +1,9 @@
+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
@@ -0,0 +1,6 @@
+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
@@ -0,0 +1,24 @@
+>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/illumina/wolf_data/wolf_F.fastq.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_F.fastq.gz
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_R.fastq.gz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_data/wolf_R.fastq.gz
--- 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
@@ -0,0 +1,8 @@
+@param,matching,strict
+@param,primer_mismatches,2
+@param,indels,false
+experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_diet_dataset.tgz
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/wolf_diet_dataset.tgz
--- 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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,102 @@
+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
@@ -0,0 +1,11 @@
+<?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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,12 @@
+<?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
@@ -0,0 +1,11 @@
+<?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/Show More
+++ b/Show More
Author	SHA1	Message	Date
Eric Coissac	021e2a3919	A pretty jupyter login	2025-11-21 14:40:46 +01:00
Eric Coissac	30b7175702	Make cleaning	2025-11-17 14:18:13 +01:00
Eric Coissac	35d275c104	Add pedagogic content	2025-11-16 14:55:30 +01:00
Eric Coissac	78156a8c95	bug des volumes utilisateurs	2025-11-16 14:55:30 +01:00
Eric Coissac	0eae496a94	Downsize the student image	2025-11-05 17:28:55 +01:00
Eric Coissac	d49592c5d4	Evolution of Unix course	2025-10-31 19:56:10 +01:00
Eric Coissac	1d0db893f1	Unix lecture - translation	2025-10-31 14:20:37 +01:00
coissac	cc0a7d446d	Merge pull request 'First complete version' (#4 ) from push-qsttonrunzsp into master Reviewed-on: #4	2025-10-16 18:49:32 +00:00
Eric Coissac	02b48e75fa	First complete version	2025-10-16 20:48:35 +02:00
coissac	57bf9934a3	Merge pull request 'Add a sftpgo server and a web server' (#3 ) from push-xmzwrlqxnvns into master Reviewed-on: #3	2025-10-15 23:03:39 +00:00
Eric Coissac	a3608759c5	Add the sftpgo server and a web server	2025-10-16 01:02:07 +02:00
coissac	ae77f71b6c	Merge pull request 'Correction of the doc' (#2 ) from push-zkpmmkmzmzwl into master Reviewed-on: #2	2025-10-15 13:37:49 +00:00
Eric Coissac	362720d93d	Correction of the doc	2025-10-15 15:16:42 +02:00
coissac	6b49ae48a3	Merge pull request 'push-svpkkstsnzoy' (#1 ) from push-svpkkstsnzoy into push-qlwkxzrrwlkv Reviewed-on: #1	2025-10-15 13:00:00 +00:00
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				`{"rule":"MORFOLOGIK_RULE_EN_US","sentence":"^\\QA password that secures access to the system\nA user number or UID (User IDentifier) that identifies the user on the machine\nA location on the hard disk to store the user's files, called Home or home\nA group of users, which allows working in groups on the machine (see later)\\E$"}`
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				.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}