Ajout des obitools

2025-10-15 07:15:05 +02:00
parent 21fc3a2c1f
commit 60130d6b42
6 changed files with 205 additions and 23 deletions
--- a/18
+++ b/18
@@ -9,6 +9,9 @@ RUN apt-get update && apt-get install -y \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
+    git \
+    build-essential \
+    curl \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

 # Install R kernel for Jupyter (as root)
@@ -16,12 +19,25 @@ RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
    R -e "IRkernel::installspec(user = FALSE)"

 # Install some useful R packages for labs
-RUN R -e "install.packages(c('ggplot2', 'dplyr', 'tidyr', 'readr'), repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages(c('tidyverse', 'vegan', 'ade4'), repos='http://cran.rstudio.com/')"

 # Install bash kernel (as root also)
 RUN pip install bash_kernel && \
    python -m bash_kernel.install --sys-prefix

+# Install obitools4 (written in Go)
+RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
+
+# Install csvkit
+RUN pip install csvkit
+
+# Install csvlens
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y \
+    && . $HOME/.cargo/env \
+    && cargo install csvlens \
+    && mv $HOME/.cargo/bin/csvlens /usr/local/bin/ \
+    && rm -rf $HOME/.cargo $HOME/.rustup
+
 # Create necessary directories with proper permissions
 RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
--- a/Readme.md
+++ b/Readme.md
@@ -113,6 +113,71 @@ Each student will see these directories in their JupyterLab:
 - **`work/`** : Personal workspace (persistent, private)
 - **`shared/`** : Shared workspace between all students (read/write)
 - **`course/`** : Course files (read-only, you deposit files)
+  - **`course/R_packages/`** : Shared R packages (read-only for students, only admin can install)
+
+### 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
+chmod +x install-r-packages-admin.sh
+
+# Install packages
+./install-r-packages-admin.sh reshape2 plotly knitr
+```
+
+This script:
+- Installs packages in the `course/R_packages/` directory
+- All students can use them (read-only)
+- No need to rebuild the image
+
+**From admin notebook:**
+
+Login as `admin` and create an R notebook:
+
+```r
+# Install packages in course directory (admin only)
+course_lib <- "/home/jovyan/course/R_packages"
+dir.create(course_lib, recursive = TRUE, showWarnings = FALSE)
+
+install.packages(c('reshape2', 'plotly', 'knitr'), 
+                 lib = course_lib,
+                 repos = 'http://cran.rstudio.com/')
+```
+
+Note: Admin account has write access to the course directory.
+
+### Using R Packages (Students)
+
+Students simply load packages normally:
+```r
+library(reshape2)  # Loads from course/R_packages/ automatically
+library(plotly)
+```
+
+R automatically finds packages in `/home/jovyan/course/R_packages/` thanks to the `R_LIBS_USER` environment variable.
+
+### List Available Packages
+
+```r
+# List all available packages
+installed.packages()[,"Package"]
+
+# Or check course packages specifically
+list.files("/home/jovyan/course/R_packages")
+```

 ### Deposit Files for Course

--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -6,7 +6,7 @@ services:
    container_name: jupyterhub
    image: jupyterhub-hub:latest
    ports:
-      - "8000:8000"
+      - "8888:8000"
    volumes:
      # Access to Docker socket to spawn student containers
      - /var/run/docker.sock:/var/run/docker.sock
@@ -20,6 +20,8 @@ services:
    environment:
      # Shared password for all students
      JUPYTERHUB_PASSWORD: metabar2025
+      # Admin password (for installing R packages)
+      JUPYTERHUB_ADMIN_PASSWORD: admin2025
      # Optional environment variables
      DOCKER_NOTEBOOK_DIR: /home/jovyan/work

--- a/install_packages.sh
+++ b/install_packages.sh
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+# Script to install R packages in the course directory (admin only)
+# Usage: ./install-r-packages.sh package1 package2 package3
+
+set -e
+
+GREEN='\033[0;32m'
+BLUE='\033[0;34m'
+YELLOW='\033[1;33m'
+RED='\033[0;31m'
+NC='\033[0m'
+
+echo -e "${BLUE}📦 R Package Installer (Admin)${NC}"
+echo "================================"
+echo ""
+
+# Check if packages are provided
+if [ $# -eq 0 ]; then
+    echo -e "${RED}❌ Error: No packages specified${NC}"
+    echo ""
+    echo "Usage:"
+    echo "  ./install-r-packages.sh package1 package2 package3"
+    echo ""
+    echo "Example:"
+    echo "  ./install-r-packages.sh reshape2 plotly knitr"
+    exit 1
+fi
+
+# Build package list
+PACKAGES=$(IFS=,; echo "$*")
+R_PACKAGES=$(echo "$PACKAGES" | sed "s/,/', '/g")
+
+echo -e "${YELLOW}📋 Packages to install: ${R_PACKAGES}${NC}"
+echo ""
+
+# Create a temporary directory for installation
+TEMP_DIR=$(mktemp -d)
+echo -e "${BLUE}📁 Creating temporary directory: ${TEMP_DIR}${NC}"
+
+# Install packages in temporary directory
+echo -e "${BLUE}🔨 Installing R packages...${NC}"
+docker run --rm \
+    --user root \
+    -v "${TEMP_DIR}:/temp_packages" \
+    jupyterhub-student:latest \
+    R -e "install.packages(c('${R_PACKAGES}'), lib='/temp_packages', repos='http://cran.rstudio.com/')" || {
+    echo -e "${RED}❌ Failed to install packages${NC}"
+    rm -rf "${TEMP_DIR}"
+    exit 1
+}
+
+# Copy to course volume
+echo ""
+echo -e "${BLUE}💾 Copying to course volume...${NC}"
+docker run --rm \
+    -v jupyterhub-course:/target \
+    -v "${TEMP_DIR}:/source" \
+    alpine sh -c "mkdir -p /target/R_packages && cp -r /source/* /target/R_packages/"
+
+# Clean up
+rm -rf "${TEMP_DIR}"
+
+# List installed packages
+echo ""
+echo -e "${GREEN}✅ Installation complete!${NC}"
+echo ""
+echo -e "${BLUE}📦 Installed packages in course/R_packages:${NC}"
+docker run --rm \
+    -v jupyterhub-course:/course \
+    alpine ls -1 /course/R_packages/
+
+echo ""
+echo -e "${YELLOW}ℹ️  Students need to restart their R kernels to use new packages.${NC}"
--- a/jupyterhub_config.py
+++ b/jupyterhub_config.py
@@ -33,19 +33,19 @@ c.DockerSpawner.remove = True
 c.DockerSpawner.name_template = "jupyter-{username}"

 # Volume mounting to persist student data
-# Set root to /home/jovyan to see all directories
-notebook_dir = '/home/jovyan'
+# Set root to work/ - everything is persistent
+notebook_dir = '/home/jovyan/work'
 c.DockerSpawner.notebook_dir = notebook_dir

-# Personal volume for each student + shared volume
+# Personal volume for each student + shared volumes under work/
 c.DockerSpawner.volumes = {
-    # Personal volume (persistent) - mounted in work/
+    # Personal volume (persistent) - root directory
    'jupyterhub-user-{username}': '/home/jovyan/work',
-    # Shared volume between all students
-    'jupyterhub-shared': '/home/jovyan/shared',
-    # Shared read-only volume for course files (optional)
+    # Shared volume between all students - under work/
+    'jupyterhub-shared': '/home/jovyan/work/shared',
+    # Shared read-only volume for course files - under work/
    'jupyterhub-course': {
-        'bind': '/home/jovyan/course',
+        'bind': '/home/jovyan/work/course',
        'mode': 'ro'  # read-only
    }
 }
@@ -54,6 +54,23 @@ c.DockerSpawner.volumes = {
 c.DockerSpawner.mem_limit = '2G'
 c.DockerSpawner.cpu_limit = 1.0

+# Environment variables for student containers
+c.DockerSpawner.environment = {
+    # R package library in read-only course directory under work/
+    'R_LIBS_USER': '/home/jovyan/work/R_packages',
+    'R_LIBS_SITE': '/home/jovyan/work/course/R_packages',
+     # Path to R packages in read-only
+    'PATH': '/home/jovyan/work/course/bin:${PATH}'
+}
+
+# Create user R lib directory 
+#async def create_user_hierarchy(spawner):
+#    cmd = "mkdir -p /home/jovyan/work/R_packages && chown jovyan:jovyan /home/jovyan/work/R_packages"
+#    spawner.extra_create_kwargs.update({'command': f"/bin/bash -c '{cmd} && start-notebook.sh'"})
+
+#c.Spawner.pre_spawn_hook = create_user_r_libs
+
+
 # User configuration - Simple password authentication for lab
 from jupyterhub.auth import DummyAuthenticator

@@ -65,12 +82,16 @@ class SimplePasswordAuthenticator(DummyAuthenticator):
        if authentication is None:
            return False
        
-        # Get password from environment variable
-        expected_password = os.environ.get('JUPYTERHUB_PASSWORD', 'metabar2025')
        provided_password = authentication.get('password', '')
        
-        # Check password
-        return provided_password == expected_password
+        # Admin user with special password
+        if username == 'admin':
+            admin_password = os.environ.get('JUPYTERHUB_ADMIN_PASSWORD', 'admin2025')
+            return provided_password == admin_password
+        
+        # Regular students with shared password
+        student_password = os.environ.get('JUPYTERHUB_PASSWORD', 'metabar2025')
+        return provided_password == student_password

 c.JupyterHub.authenticator_class = SimplePasswordAuthenticator

@@ -125,7 +146,7 @@ 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'
+notebook_dir = '/home/jovyan/work'
 c.DockerSpawner.notebook_dir = notebook_dir

 # Volume personnel pour chaque étudiant + volume partagé
@@ -133,10 +154,10 @@ 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',
+    'jupyterhub-shared': '/home/jovyan/work/shared',
    # Volume partagé en lecture seule pour les fichiers du cours (optionnel)
    'jupyterhub-course': {
-        'bind': '/home/jovyan/course',
+        'bind': '/home/jovyan/work/course',
        'mode': 'ro'  # read-only
    }
 }
--- a/setup.sh
+++ b/setup.sh
@@ -61,16 +61,20 @@ if docker ps | grep -q jupyterhub; then
    echo -e "${GREEN}✅ JupyterHub is running!${NC}"
    echo ""
    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
-    echo -e "${GREEN}🌐 JupyterHub available at: http://localhost:8000${NC}"
+    echo -e "${GREEN}🌐 JupyterHub available at: http://localhost:8888${NC}"
    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
    echo ""
    echo "📝 Password: metabar2025"
    echo "👥 Students can connect with any username"
    echo ""
+    echo "🔑 Admin account:"
+    echo "   Username: admin"
+    echo "   Password: admin2025"
+    echo ""
    echo "📂 Each student will have access to:"
-    echo "   - work/   : personal workspace"
-    echo "   - shared/ : shared workspace"
-    echo "   - course/ : course files (read-only)"
+    echo "   - work/        : personal workspace (everything here is saved)"
+    echo "   - work/shared/ : shared workspace"
+    echo "   - work/course/ : course files (read-only)"
    echo ""
    echo "🔍 To view logs:    docker-compose logs -f jupyterhub"
    echo "🛑 To stop:         docker-compose down"