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
439 changed files with 1256590 additions and 351 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$"}
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "git.enabled": false
+}
--- a/34
+++ b/34
@@ -1,34 +0,0 @@
-FROM jupyter/base-notebook:latest
-
-USER root
-
-# Installation de R et des dépendances système
-RUN apt-get update && apt-get install -y \
-    r-base \
-    r-base-dev \
-    libcurl4-openssl-dev \
-    libssl-dev \
-    libxml2-dev \
-    texlive-xetex \
-    texlive-fonts-recommended \
-    texlive-plain-generic \
-    && apt-get clean && rm -rf /var/lib/apt/lists/*
-
-# Installation du kernel R pour Jupyter (en tant que root)
-RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
-    R -e "IRkernel::installspec(user = FALSE)"
-
-# Installation de quelques packages R utiles pour les TP
-RUN R -e "install.packages(c('tidyverse','vegan','ade4'), repos='http://cran.rstudio.com/')"
-
-# Installation du kernel bash (en tant que root aussi)
-RUN pip install bash_kernel && \
-    python -m bash_kernel.install --sys-prefix
-
-# Créer les répertoires nécessaires avec les bonnes permissions
-RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
-    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
-
-USER ${NB_UID}
-
-WORKDIR /home/${NB_USER}
--- a/Readme.md
+++ b/Readme.md
@@ -1,258 +1,369 @@
-# Configuration JupyterHub avec OrbStack sur Mac (tout en Docker)
+# JupyterHub Configuration with OrbStack on Mac (all in Docker)

-## Prérequis
- OrbStack installé et démarré
+## Prerequisites

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

-Votre dossier `~/jupyterhub-tp` doit contenir :
-```
-~/jupyterhub-tp/
-├── Dockerfile                  # Image pour les étudiants (déjà créée)
-├── Dockerfile.hub              # Image pour JupyterHub (nouvelle)
-├── jupyterhub_config.py        # Configuration
-└── docker-compose.yml          # Orchestration
-```
+-   On MacOS, [OrbStack](https://orbstack.dev/ "A Docker implementation optimised for MacOS") is recommanded

-## Étapes d'installation
+## Installation Steps

-### 1. Créer la structure de dossiers
+### 1. Create Directory Structure

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

-### 2. Créer tous les fichiers nécessaires
-
-Créez les fichiers suivants avec le contenu des artifacts :
- `Dockerfile` (artifact "Dockerfile pour JupyterHub avec R et Bash")
- `Dockerfile.hub` (artifact "Dockerfile pour le container JupyterHub")
- `jupyterhub_config.py` (artifact "Configuration JupyterHub")
- `docker-compose.yml` (artifact "docker-compose.yml")
-
-### 3. Construire les images Docker
+Enter into the `OBIJupyterHub` directory

 ```bash
-# Image pour les étudiants
-docker build -t jupyterhub-student:latest -f Dockerfile .
-
-# Image pour le hub JupyterHub
-docker build -t jupyterhub-hub:latest -f Dockerfile.hub .
+cd OBIJupyterHub
 ```

-### 4. Démarrer JupyterHub avec Docker Compose
+#### File Structure

-```bash
-docker-compose up -d
+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
 ```

-### 5. Accéder à JupyterHub
+### 2. Start JupyterHub

-Ouvrez votre navigateur et allez à : **http://localhost:8000**
+From the terminal, in the `OBIJupyterHub` directory, run the following command:

-Vous pouvez vous connecter avec n'importe quel nom d'utilisateur.
+``` bash
+./start-jupyterhub.sh
+```

-## Commandes utiles
+### 3. Access JupyterHub

-### Voir les logs de JupyterHub
-```bash
+Open your browser and go to: **http://localhost:8888**
+
+You can log in as a student with any username and password: `metabar2025`
+
+## Useful Commands
+
+### View JupyterHub logs
+
+``` bash
+cd obijupyterhub
 docker-compose logs -f jupyterhub
 ```

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

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

-### Redémarrer JupyterHub (après modification du config)
-```bash
+### Restart JupyterHub (after config modification)
+
+``` bash
+cd obijupyterhub
 docker-compose restart jupyterhub
 ```

-### Reconstruire après modification du Dockerfile
-```bash
-# Pour l'image étudiants
-docker build -t jupyterhub-student:latest -f Dockerfile .
-docker-compose restart jupyterhub
+### View logs for a specific student

-# Pour l'image hub
-docker-compose up -d --build
+``` bash
+docker logs jupyter-<username>
 ```

-### Voir les logs d'un étudiant spécifique
-```bash
-docker logs jupyter-nom_utilisateur
-```
+Replace `<username>` by the actual username of the student.

-### Nettoyer après le TP
-```bash
-# Arrêter et supprimer tous les containers
+### Clean up after lab
+
+``` bash
+# Stop and remove all containers
+cd obijupyterhub
 docker-compose down

-# Supprimer les containers étudiants
+# Remove student containers
 docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f

-# Supprimer les volumes (ATTENTION : supprime les données étudiants)
+# Remove volumes (WARNING: deletes student data)
 docker volume ls | grep jupyterhub-user | awk '{print $2}' | xargs docker volume rm

-# Tout nettoyer (containers + volumes + réseau)
+# Clean everything (containers + volumes + network)
 docker-compose down -v
 docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
 docker volume prune -f
 ```

-## Gestion des données partagées
+## Managing Shared Data

-### Structure des dossiers pour chaque étudiant
+### Directory Structure for Each Student

-Chaque étudiant verra ces dossiers dans son JupyterLab :
- **`work/`** : Son espace personnel (persistant, privé)
- **`shared/`** : Espace partagé entre tous les étudiants (lecture/écriture)
- **`course/`** : Fichiers du cours (lecture seule, vous déposez les fichiers)
+Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):

-### Déposer des fichiers pour le cours
+```         
+work/                             # Personal workspace root (persistent)
+├── [student files]               # Their own files and notebooks
+├── R_packages/                   # Personal R packages (writable by student)
+├── shared/                       # Shared workspace (read/write, shared with all)
+└── course/                       # Course files (read-only, managed by admin)
+    ├── R_packages/               # Shared R packages (read-only, installed by prof)
+    ├── bin/                      # Shared executables (in PATH)
+    └── [course materials]        # Your course files
+```

-Pour mettre des fichiers dans le dossier `course/` (accessible en lecture seule) :
+**R Package Priority:** 

-```bash
-# Créer un dossier temporaire
+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`) 
+- Can write to `course/` directory
+
+**Student Accounts:** 
+
+- Username: any name 
+- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`) 
+- Read-only access to `course/` directory
+
+### Installing R Packages (Admin Only)
+
+**From your Mac (recommended):**
+
+``` bash
+# Install packages
+tools/install_packages.sh reshape2 plotly knitr
+```
+
+This script: - Installs packages in the `course/R_packages/` directory - All students can use them (read-only) - No need to rebuild the image
+
+**Students can also install their own packages:**
+
+Students can install packages in their personal `work/R_packages/`:
+
+```r
+# Install in personal library (each student has their own)
+install.packages('mypackage')  # Will install in work/R_packages/
+```
+
+### Using R Packages (Students)
+
+Students simply load packages normally:
+
+``` 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) 
+1. Prof packages: `/home/jovyan/work/course/R_packages/` (R_LIBS_SITE) 
+1. System packages
+
+### List Available Packages
+
+``` r
+# List all available packages (personal + course + system)
+installed.packages()[,"Package"]
+
+# Check personal packages
+list.files("/home/jovyan/work/R_packages")
+
+# Check course packages (installed by prof)
+list.files("/home/jovyan/work/course/R_packages")
+```
+
+### Deposit Files for Course
+
+To put files in the `course/` directory (accessible read-only):
+
+``` bash
+# Create a temporary directory
 mkdir -p ~/jupyterhub-tp/course-files

-# Copier vos fichiers dedans
-cp mes_notebooks.ipynb ~/jupyterhub-tp/course-files/
-cp mes_donnees.csv ~/jupyterhub-tp/course-files/
+# Copy your files into it
+cp my_notebooks.ipynb ~/jupyterhub-tp/course-files/
+cp my_data.csv ~/jupyterhub-tp/course-files/

-# Copier dans le volume Docker
+# Copy into Docker volume
 docker run --rm \
  -v jupyterhub-course:/target \
  -v ~/jupyterhub-tp/course-files:/source \
  alpine sh -c "cp -r /source/* /target/"
 ```

-### Accéder aux fichiers partagés entre étudiants
+### Retrieve Student Work

-Les étudiants peuvent collaborer via le dossier `shared/` :
+``` bash
+# List user volumes
+docker volume ls | grep 'obijupyterhub_user-'

-```python
-# Dans un notebook, pour lire un fichier partagé
-import pandas as pd
-df = pd.read_csv('/home/jovyan/shared/donnees_groupe.csv')
-
-# Pour écrire un fichier partagé
-df.to_csv('/home/jovyan/shared/resultats_alice.csv')
-```
-
-### Récupérer les travaux des étudiants
-
-```bash
-# Lister les volumes utilisateurs
-docker volume ls | grep jupyterhub-user
-
-# Copier les fichiers d'un étudiant spécifique
+# Copy files from a specific student
 docker run --rm \
-  -v jupyterhub-user-alice:/source \
-  -v ~/rendus:/target \
+  -v obijupyterhub_user-alice:/source \
+  -v ~/submissions:/target \
  alpine sh -c "cp -r /source/* /target/alice/"

-# Copier tous les travaux partagés
+# Copy all shared work
 docker run --rm \
-  -v jupyterhub-shared:/source \
-  -v ~/rendus/shared:/target \
+  -v obijupyterhub_shared:/source \
+  -v ~/submissions/shared:/target \
  alpine sh -c "cp -r /source/* /target/"
 ```

-## Gestion des utilisateurs
+## User Management

-### Option 1 : Liste d'utilisateurs prédéfinis
-Dans `jupyterhub_config.py`, décommentez et modifiez :
-```python
-c.Authenticator.allowed_users = {'etudiant1', 'etudiant2', 'etudiant3'}
+### Option 1: Predefined User List
+
+In `jupyterhub_config.py`, uncomment and modify:
+
+``` python
+c.Authenticator.allowed_users = {'student1', 'student2', 'student3'}
 ```

-### Option 2 : Autoriser tout le monde (pour tests)
-Par défaut, la configuration autorise n'importe quel utilisateur :
-```python
+### Option 2: Allow Everyone (for testing)
+
+By default, the configuration allows any user:
+
+``` python
 c.Authenticator.allow_all = True
 ```

-⚠️ **Attention** : DummyAuthenticator est UNIQUEMENT pour les tests locaux !
+⚠️ **Warning**: DummyAuthenticator is ONLY for local testing!

-## Vérification des kernels
+## Kernel Verification

-Une fois connecté, créez un nouveau notebook et vérifiez que vous avez accès à :
- **Python 3** (kernel par défaut)
- **R** (kernel R)
- **Bash** (kernel bash)
+Once logged in, create a new notebook and verify you have access to: 

-## Personnalisation pour vos TP
+- **Python 3** (default kernel) 
+- **R** (R kernel) 
+- **Bash** (bash kernel)

-### Ajouter des packages R supplémentaires
-Modifiez le `Dockerfile` (avant `USER ${NB_UID}`) :
-```dockerfile
-RUN R -e "install.packages(c('votre_package'), repos='http://cran.rstudio.com/')"
+## Customization for Your Labs
+
+### Add Additional R Packages
+
+Modify the `Dockerfile` (before `USER ${NB_UID}`):
+
+``` dockerfile
+RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
 ```

-Puis reconstruisez :
+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
 ```

-### Ajouter des packages Python
-Ajoutez dans le `Dockerfile` (avant `USER ${NB_UID}`) :
-```dockerfile
+### Add Python Packages
+
+Add to the `Dockerfile` (before `USER ${NB_UID}`):
+
+``` dockerfile
 RUN pip install numpy pandas matplotlib seaborn
 ```

-### Distribuer des fichiers aux étudiants
-Créez un dossier `files_tp/` et ajoutez dans le `Dockerfile` :
-```dockerfile
-COPY files_tp/ /home/${NB_USER}/tp/
-RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/tp
+### Distribute Files to Students
+
+Create a `files_lab/` directory and add to the `Dockerfile`:
+
+``` dockerfile
+COPY files_lab/ /home/${NB_USER}/lab/
+RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
 ```

-### Changer le port (si 8000 est occupé)
-Modifiez dans `docker-compose.yml` :
-```yaml
+### Change Port (if 8000 is occupied)
+
+Modify in `docker-compose.yml`:
+
+``` yaml
 ports:
-  - "8001:8000"  # Accessible sur localhost:8001
+  - "8001:8000"  # Accessible on localhost:8001
 ```

-## Avantages de cette approche
+## Advantages of This Approach

-✅ **Tout en Docker** : Plus besoin d'installer Python/JupyterHub sur votre Mac  
-✅ **Portable** : Facile à déployer sur un autre Mac ou serveur  
-✅ **Isolé** : Pas de pollution de votre environnement système  
-✅ **Facile à nettoyer** : Un simple `docker-compose down` suffit  
-✅ **Reproductible** : Les étudiants auront exactement le même environnement
+✅ **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

-## Dépannage
+## Troubleshooting

-**Erreur "Cannot connect to Docker daemon"** :
- Vérifiez qu'OrbStack est démarré
- Vérifiez que le socket existe : `ls -la /var/run/docker.sock`
+**Error "Cannot connect to Docker daemon"**: 

-**Les containers étudiants ne démarrent pas** :
- Vérifiez les logs : `docker-compose logs jupyterhub`
- Vérifiez que l'image étudiants existe : `docker images | grep jupyterhub-student`
+- Check that OrbStack is running 
+- Verify the socket exists: `ls -la /var/run/docker.sock`

-**Port 8000 déjà utilisé** :
- Changez le port dans `docker-compose.yml`
+**Student containers don't start**: 

-**Après modification du config, les changements ne sont pas pris en compte** :
-```bash
-docker-compose restart jupyterhub
-```
+- Check logs: `docker-compose logs jupyterhub` 
+- Verify student image exists: `docker images | grep jupyterhub-student`

-**Je veux repartir de zéro** :
-```bash
+**Port 8000 already in use**: 
+
+- Change port in `docker-compose.yml`
+
+
+**I want to start from scratch**:
+
+``` bash
+push obijupyterhub
 docker-compose down -v
 docker rmi jupyterhub-hub jupyterhub-student
-# Puis reconstruire tout
+popd
+
+# Then rebuild everything
+./start-jupyterhub.sh
 ```
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -1,34 +0,0 @@
-services:
-  jupyterhub:
-    build:
-      context: .
-      dockerfile: Dockerfile.hub
-    container_name: jupyterhub
-    image: jupyterhub-hub:latest
-    ports:
-      - "8888:8000"
-    volumes:
-      # Accès au socket Docker pour spawner les containers étudiants
-      - /var/run/docker.sock:/var/run/docker.sock
-      # Persistance de la base de données JupyterHub
-      - jupyterhub-data:/srv/jupyterhub
-      # Montage du fichier de config en direct (pour modifications faciles)
-      - ./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
-    networks:
-      - jupyterhub-network
-    restart: unless-stopped
-    environment:
-      # Mot de passe partagé pour tous les étudiants
-      JUPYTERHUB_PASSWORD: metabar2025
-      # Variables d'environnement optionnelles
-      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_config.py
+++ b/jupyterhub_config.py
@@ -1,91 +0,0 @@
-import os
-
-# Configuration de base
-c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner'
-
-# Activer les logs de debug
-c.JupyterHub.log_level = 'DEBUG'
-c.Spawner.debug = True
-
-# Image Docker à utiliser pour les containers étudiants
-c.DockerSpawner.image = 'jupyterhub-student:latest'
-
-# Réseau Docker (créez-le avec: docker network create jupyterhub-network)
-c.DockerSpawner.network_name = 'jupyterhub-network'
-
-# Connexion au socket Docker d'OrbStack depuis le container hub
-c.DockerSpawner.client_kwargs = {'base_url': 'unix:///var/run/docker.sock'}
-
-# IMPORTANT : URL interne pour communiquer entre containers
-# Le hub container communique avec les user containers via le réseau Docker
-c.JupyterHub.hub_ip = '0.0.0.0'
-c.JupyterHub.hub_connect_ip = 'jupyterhub'
-
-# Configuration réseau pour les containers étudiants
-c.DockerSpawner.use_internal_ip = True
-c.DockerSpawner.network_name = 'jupyterhub-network'
-c.DockerSpawner.extra_host_config = {'network_mode': 'jupyterhub-network'}
-
-# Supprimer les containers après déconnexion (optionnel, mettre False pour garder les containers)
-c.DockerSpawner.remove = True
-
-# Nommage des containers
-c.DockerSpawner.name_template = "jupyter-{username}"
-
-# Montage de volumes pour persister les données des étudiants
-# Définir la racine à /home/jovyan pour voir tous les dossiers
-notebook_dir = '/home/jovyan'
-c.DockerSpawner.notebook_dir = notebook_dir
-
-# Volume personnel pour chaque étudiant + volume partagé
-c.DockerSpawner.volumes = {
-    # Volume personnel (persistant) - monté dans work/
-    'jupyterhub-user-{username}': '/home/jovyan/work',
-    # Volume partagé entre tous les étudiants
-    'jupyterhub-shared': '/home/jovyan/shared',
-    # Volume partagé en lecture seule pour les fichiers du cours (optionnel)
-    'jupyterhub-course': {
-        'bind': '/home/jovyan/course',
-        'mode': 'ro'  # read-only
-    }
-}
-
-# Configuration de la mémoire et CPU (ajustez selon vos besoins)
-c.DockerSpawner.mem_limit = '2G'
-c.DockerSpawner.cpu_limit = 1.0
-
-# Configuration des utilisateurs - Mot de passe simple pour TP
-from jupyterhub.auth import DummyAuthenticator
-
-class SimplePasswordAuthenticator(DummyAuthenticator):
-    """Authentificateur simple avec un mot de passe partagé pour tous"""
-    
-    def check_allowed(self, username, authentication=None):
-        """Vérifie si l'utilisateur est autorisé"""
-        if authentication is None:
-            return False
-        
-        # Récupérer le mot de passe depuis la variable d'environnement
-        expected_password = os.environ.get('JUPYTERHUB_PASSWORD', 'metabar2025')
-        provided_password = authentication.get('password', '')
-        
-        # Vérifier le mot de passe
-        return provided_password == expected_password
-
-c.JupyterHub.authenticator_class = SimplePasswordAuthenticator
-
-# Pour créer une liste d'utilisateurs autorisés, décommentez et modifiez:
-# c.Authenticator.allowed_users = {'etudiant1', 'etudiant2', 'etudiant3'}
-
-# Ou autoriser n'importe quel utilisateur avec le bon mot de passe:
-c.Authenticator.allow_all = True
-
-# Configuration admin
-c.Authenticator.admin_users = {'admin'}
-
-# Port d'écoute
-c.JupyterHub.bind_url = 'http://0.0.0.0:8000'
-
-# Timeout
-c.Spawner.start_timeout = 300
-c.Spawner.http_timeout = 120
--- 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/
--- a/jupyterhub_volumes/web/img/welcome_metabar.webp
+++ b/jupyterhub_volumes/web/img/welcome_metabar.webp
--- a/jupyterhub_volumes/web/index.html
+++ b/jupyterhub_volumes/web/index.html
@@ -0,0 +1,206 @@
+<!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;
+    }
+
+    /* Sidebar */
+    nav {
+        width: 250px;
+        background-color: #2c3e50;
+        color: white;
+        display: flex;
+        flex-direction: column;
+        justify-content: space-between;
+        padding: 20px 0;
+        overflow-y: auto;
+    }
+
+    nav ul {
+        list-style: none;
+        padding-left: 15px;
+        margin: 0;
+    }
+
+    nav li {
+        margin: 4px 0;
+    }
+
+    nav a {
+        color: white;
+        text-decoration: none;
+        display: block;
+        padding: 4px 8px;
+        border-radius: 4px;
+        font-weight: 500;
+    }
+
+    nav a:hover {
+        background-color: #34495e;
+    }
+
+    /* Toggle icons */
+    .folder {
+        cursor: pointer;
+        font-weight: bold;
+        display: flex;
+        align-items: center;
+    }
+
+    .folder::before {
+        content: "▸";
+        display: inline-block;
+        margin-right: 6px;
+        transition: transform 0.2s ease;
+    }
+
+    .folder.open::before {
+        transform: rotate(90deg);
+    }
+
+    ul.collapsed {
+        display: none;
+    }
+
+    /* Admin links */
+    nav .admin-links {
+        border-top: 1px solid #34495e;
+        margin-top: 10px;
+        padding-top: 10px;
+    }
+
+    /* Main content */
+    main {
+        flex: 1;
+        display: flex;
+        flex-direction: column;
+        overflow: hidden;
+        align-items: center;
+        background-color: #f7f7f7;
+    }
+
+    header img {
+        width: 100%;
+        max-width: 1000px;
+        height: auto;
+        display: block;
+    }
+
+    iframe#content-frame {
+        flex: 1;
+        width: 100%;
+        border: none;
+        max-width: 1000px;
+        background-color: white;
+    }
+
+    nav::-webkit-scrollbar {
+        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;
+
+            const subUl = document.createElement("ul");
+            subUl.classList.add("collapsed");
+
+            folder.addEventListener("click", () => {
+                folder.classList.toggle("open");
+                subUl.classList.toggle("collapsed");
+            });
+
+            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
+++ b/jupyterhub_volumes/web/obidoc/404.html
@@ -0,0 +1,56 @@
+<!DOCTYPE html>
+<html lang="en">
+
+  <head>
+    <meta charset="UTF-8">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<meta name="description" content="">
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+++ 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
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+    <title>Exact alignment on OBITools4 documentation</title>
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+    <description>Recent content in Exact alignment on OBITools4 documentation</description>
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+++ 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
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+    <generator>Hugo</generator>
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--- a/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/basics/index.xml
@@ -0,0 +1,12 @@
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+  <channel>
+    <title>Basics on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/basics/</link>
+    <description>Recent content in Basics on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/basics/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/demultiplexing/index.xml
@@ -0,0 +1,12 @@
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+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>Demultiplexing samples on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/demultiplexing/</link>
+    <description>Recent content in Demultiplexing samples on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/demultiplexing/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/experimental/index.xml
@@ -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>Experimentals on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/experimental/</link>
+    <description>Recent content in Experimentals on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/experimental/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/index.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>The OBITools4 commands on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/docs/commands/</link>
+    <description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/docs/commands/index.xml" rel="self" type="application/rss+xml" />
+    <item>
+      <title>Glossary of tags</title>
+      <link>http://metabar:8888/obidoc/docs/commands/tags/</link>
+      <pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
+      <guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
+      <description>&lt;h1 id=&#34;glossary-of-tags&#34;&gt;&#xA;  Glossary of tags&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#glossary-of-tags&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h1&gt;&#xA;&lt;h3 id=&#34;--d--&#34;&gt;&#xA;  - D -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--d--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;definition&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;text information about the sequence present in the original sequence file.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;direction&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3 id=&#34;--f--&#34;&gt;&#xA;  - F -&#xA;  &lt;a class=&#34;anchor&#34; href=&#34;#--f--&#34;&gt;#&lt;/a&gt;&#xA;&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_error&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Number of mismatch between forward primer and priming site&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_match&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer priming site sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&#xA;&lt;p&gt;&lt;strong&gt;forward_primer&lt;/strong&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Forward primer sequence&#xA;(&#xA;  &lt;a href=&#34;http://metabar:8888/obidoc/obitools/obipcr/&#34;&gt;obipcr&lt;/a&gt;)&lt;/p&gt;</description>
+    </item>
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.html
--- a/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
+++ b/jupyterhub_volumes/web/obidoc/docs/commands/options/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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+  <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}}
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--- 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 @@
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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
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+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
@@ -0,0 +1,24 @@
+>seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
+gcctgaaactcaaaggacttggcggtgctttacatccct
+>seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
+>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
+ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
+gattaaacctcaaaggacttggcagtgctttatacccct
+>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
+agcttaaaactcaaaggacttggcggtgctttataccctt
+>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
+gcttaaaactcaaaggacttggcggtgctttatatccct
--- a/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
+++ b/jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
@@ -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/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
Eric Coissac	64cb75e40a	Image multistage	2025-10-15 14:58:46 +02:00
Eric Coissac	60130d6b42	Ajout des obitools	2025-10-15 09:06:58 +02:00
Eric Coissac	21fc3a2c1f	Traduction en anglais des fichiers	2025-10-15 07:14:53 +02:00
				`@@ -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$"}`
				`@@ -0,0 +1 @@`
				.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}