Add dockerfile (#2)

.github/workflows/publish-docker.yaml

@@ -0,0 +1,20 @@
+name: Publish Docker image
+
+on:
+  push:
+    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

@@ -0,0 +1,36 @@
+# Use the bioconductor base image as the starting point
+FROM --platform=linux/amd64 python:3.11-slim
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y \
+    wget \
+    build-essential \
+    rsync
+
+# Install Python dependencies
+COPY requirements.txt /requirements.txt
+RUN pip install -r /requirements.txt
+
+# 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 && \
+    cd sqlite-autoconf-3450300 && \
+    ./configure && \
+    make && \
+    make install && \
+    export PATH="/usr/local/lib:$PATH" && \
+    cd .. && \
+    rm -rf sqlite-autoconf-3450300.tar.gz sqlite-autoconf-3450300
+
+# Set environment variable for LD_LIBRARY_PATH
+ENV LD_LIBRARY_PATH=/usr/local/lib
+
+# Copy the project files into the Docker image 
+COPY . /project
+
+# Set the working directory
+WORKDIR /project
+
+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