Merge pull request #24 from WEHI-ResearchComputing/docker-recurse

Fix container dependencies

Author: edoyango

.github/workflows/singularity.yml

@@ -49,9 +49,7 @@ jobs:
 
       - name: Login and Deploy Container
         if: (github.event_name != 'pull_request')
-        run: |         
-            if [[ "${keepgoing}" == "true" ]]; then
-                echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
-                container_name=$(echo ${GITHUB_REPOSITORY} | tr '[:upper:]' '[:lower:]')
-                singularity push container.sif oras://ghcr.io/${container_name}:${tag}
-            fi
+        run: |
+            echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
+            container_name=$(echo ${GITHUB_REPOSITORY} | tr '[:upper:]' '[:lower:]')
+            singularity push container.sif oras://ghcr.io/${container_name}:${tag}

Dockerfile

@@ -3,8 +3,9 @@ FROM python:3.9.19-slim-bookworm
 COPY pyproject.toml /opt/PartiNet/pyproject.toml
 COPY partinet /opt/PartiNet/partinet
 
+RUN apt-get update && apt-get install libglib2.0-0 libxext6 libx11-6 -y && rm -rf /var/cache/apt/archives /var/lib/apt/lists/* && apt-get clean
 RUN python -m pip install --no-cache-dir --no-cache /opt/PartiNet
 
 LABEL AUTHORS Mihin Perera, Edward Yang, Julie Iskander
 LABEL MAINTAINERS Mihin Perera, Edward Yang, Julie Iskander
-LABEL VERSION v0.0.01
+LABEL VERSION v0.1.1

Singularity

@@ -5,9 +5,17 @@ from: python:3.9.19-slim-bookworm
   . /opt/PartiNet
 
 %post
+  # install system dependencies
+  apt-get update
+  apt-get install libglib2.0-0 libxext6 libx11-6 -y
+
+  # cleanup apt package index
+  rm -rf /var/cache/apt/archives /var/lib/apt/lists/*
+  apt-get clean
+
   python -m pip install --no-cache-dir /opt/PartiNet
 
 %labels
   AUTHORS Mihin Perera, Edward Yang, Julie Iskander
   MAINTAINERS Mihin Perera, Edward Yang, Julie Iskander
-  VERSION v0.0.01
+  VERSION v0.1.1