Add docker image

.github/workflows/publish-docker.yaml

@@ -0,0 +1,23 @@
+name: Publish Docker image
+
+on:
+    push:
+        tags:
+        - '*'
+        branches:
+        - master
+    workflow_dispatch:
+
+  jobs:
+    publish_docker:
+      runs-on: ubuntu-latest
+      steps:
+        - name: Checkout
+          uses: actions/checkout@v3
+        - name: Publish to Registry
+          uses: elgohr/Publish-Docker-Github-Action@v5
+          with:
+            name: ${{ github.repository }}/builder:${{ github.ref_name }}
+            username: ${{ github.actor }}
+            password: ${{ secrets.GITHUB_TOKEN }}
+            registry: ghcr.io

.github/workflows/publish_python.yml

@@ -5,7 +5,7 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
-  
+
 jobs:
   build-deploy:
     runs-on: ubuntu-latest

Dockerfile

@@ -1,5 +1,5 @@
 # Use the bioconductor base image as the starting point
-FROM --platform=linux/amd64 bioconductor/bioconductor_docker:devel
+FROM --platform=linux/amd64 python:3.11-slim
 
 # Install system dependencies
 RUN apt-get update && \
@@ -8,25 +8,10 @@ RUN apt-get update && \
     build-essential \
     rsync
 
-# Install Quarto CLI
-RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.43/quarto-1.5.43-linux-amd64.deb && \
-    dpkg -i quarto-1.5.43-linux-amd64.deb && \
-    rm quarto-1.5.43-linux-amd64.deb
-
-# Install TinyTeX
-RUN quarto install tinytex
-
 # Install Python dependencies
 COPY requirements.txt /requirements.txt
 RUN pip install -r /requirements.txt
 
-# Set R environment variable
-ENV R_PKG_DIR=${R_HOME}/site-library
-
-# Copy and install R packages
-COPY rpackages.R /rpackages.R
-RUN Rscript /rpackages.R
-
 # Download and build SQLite3 from source
 RUN wget --no-check-certificate https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz && \
     tar -xvf sqlite-autoconf-3450300.tar.gz && \
@@ -47,4 +32,5 @@ COPY . /project
 # Set the working directory
 WORKDIR /project
 
-RUN quarto render --execute --to html --output-dir build
+EXPOSE 8889
+CMD ["jupyter", "lab", "--allow-root", "--ip=0.0.0.0", "--port=8889", "--no-browser"]

README.md

@@ -20,4 +20,13 @@ Rscript rpackages.R
 qurto preview
 ```
 
-Take advantage of GitHub actions, which are available to automatically publish the tutorial book whenever changes are made on the **master** branch.
+GitHub actions automatically publish the tutorial book whenever changes are made on the **master** branch.
+
+## Dockerfile
+
+To build the docker image, (defaults to port 8889)
+
+```sh
+docker build -t bioc .
+docker run -it -p 8889:8889 bioc
+```

requirements.txt

@@ -10,10 +10,10 @@ singler>=0.2.0
 numpy
 scipy
 pandas
+jupyterlab
 jupyter
 jupyter-cache
 rich
-jupyterlab
 seaborn
 session-info
 celldex