Merge pull request #238 from sigven/patch1

Restructure installation doc

.github/workflows/apptainer.yaml

@@ -3,10 +3,10 @@ name: apptainer
 on:
   push:
     branches:
-      - apptainer
+      - patch1
 
 env:
-  VERSION: '1.4.1.9006' # versioned by bump2version
+  VERSION: '1.4.1.9015' # versioned by bump2version
 jobs:
   docker2apptainer:
     name: Docker2apptainer
@@ -35,31 +35,31 @@ jobs:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: 🐳 Docker img build and push to DockerHub
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: . # yes, dot
           push: false
-          load: true
           platforms: linux/amd64
           tags: |
             sigven/pcgr:${{ env.VERSION }}
+          outputs: type=docker,dest=pcgr_${{ env.VERSION }}.tar
 
       - name: Apptainer setup
         uses: eWaterCycle/setup-apptainer@v2
 
       - name: Apptainer build
         run: |
           docker image ls -a
-          docker save sigven/pcgr:${VERSION} -o pcgr_${VERSION}.tar
+          #docker save sigven/pcgr:${VERSION} -o pcgr_${VERSION}.tar
           ls -la
           df -h
           echo "Building Apptainer SIF"
           echo "---------------------------------"
-          apptainer build pcgr_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar
+          apptainer build pcgr_singularity_${VERSION}.sif docker-archive://pcgr_${VERSION}.tar
           echo "---------------------------------"
           ls -la
           df -h
-      - name: Upload SIF to GHCR
-        run: |
-          echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io
-          apptainer push pcgr_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}
+     #- name: Upload SIF to GHCR
+     #  run: |
+     #    echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+     #    apptainer push pcgr_${VERSION}.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${VERSION}

Dockerfile

@@ -1,16 +1,19 @@
 FROM ubuntu:20.04
-LABEL maintainer="https://github.com/pdiakumis"
+LABEL org.opencontainers.image.authors='[email protected], [email protected]' \
+      org.opencontainers.image.description='Personal Cancer Genome Reporter (PCGR)' \
+      org.opencontainers.image.source='https://github.com/sigven/pcgr' \
+      org.opencontainers.image.url='https://github.com/sigven/pcgr' \
+      org.opencontainers.image.documentation='https://sigven.github.io/pcgr' \
+      org.opencontainers.image.licenses='MIT'
 
 ARG MINI_VERSION=4.11.0-0
 ARG MINI_URL=https://github.com/conda-forge/miniforge/releases/download/${MINI_VERSION}/Mambaforge-${MINI_VERSION}-Linux-x86_64.sh
 
 # install core pkgs, mambaforge
 RUN apt-get update && \
     apt-get install --yes --no-install-recommends \
-    bash bzip2 curl git less vim wget zip ca-certificates && \
+    bash bzip2 curl less wget zip ca-certificates && \
     apt-get clean && \
-    rm -r /var/lib/apt/lists/* && \
-    rm -r /var/cache/apt/* && \
     curl --silent -L "${MINI_URL}" -o "mambaforge.sh" && \
     /bin/bash mambaforge.sh -b -p /opt/mambaforge/ && \
     rm mambaforge.sh

conda/env/yml/pkgdown.yml

@@ -7,4 +7,5 @@ dependencies:
   - pcgr::r-pcgrr ==1.4.1.9015 # versioned by bump2version
   - r-pkgdown
   - r-readr
+  - r-glue
   - pandoc