feat: create initial charlie-specific docker recipes

.github/workflows/docker.yml

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+name: docker
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "docker/**"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "docker/**"
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix-metadata: ${{ steps.metadata.outputs.matrix }}
+    steps:
+      - uses: hellofresh/action-changed-files@v3
+        id: metadata
+        with:
+          pattern: docker/(?P<image_dir>\w+)/.*
+          default-patterns: |
+            meta.yml
+            Dockerfile
+            environment.txt
+
+  update-docker:
+    needs: [generate-matrix]
+    strategy:
+      matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
+    if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/[email protected]
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
+      - name: Get date
+        id: date
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
+      - name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: docker/${{ matrix.image_dir }}
+          # only push container to docker hub if not triggered from a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.date.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}

docker/dcc/Dockerfile

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+FROM nciccbr/ccbr_ubuntu_base_20.04:v6
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install conda packages
+COPY environment.txt /data2/
+RUN mamba install -c conda-forge -c bioconda --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# install DCC
+ENV DCC_VERSION=v0.5.0
+RUN wget https://github.com/dieterich-lab/DCC/archive/refs/tags/v0.5.0.tar.gz && \
+    tar -xzf DCC-${DCC_VERSION}.tar.gz && \
+    cd DCC-${DCC_VERSION} && \
+    python setup.py install
+RUN which DCC && DCC -h
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

docker/dcc/environment.txt

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+python=2.7

docker/dcc/meta.yml

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+dockerhub_namespace: nciccbr
+image_name: charlie_dcc_py27
+version: v0.1.0
+container: "$(dockerhub_namespace)/$(image_name):$(version)"

docker/nclscan_py27/Dockerfile

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+FROM nciccbr/ccbr_ubuntu_base_20.04:v6
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install conda packages
+COPY environment.txt /data2/
+RUN mamba install -c conda-forge -c bioconda --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

docker/nclscan_py27/environment.txt

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+python=2.7
+bedtools=2.29.0
+blat=35
+bowtie2=2.5.1
+bwa=0.7.17
+samtools=1.15.1
+novocraft=4.03.05

docker/nclscan_py27/meta.yml

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+dockerhub_namespace: nciccbr
+image_name: charlie_nclscan_py27
+version: v0.1.0
+container: "$(dockerhub_namespace)/$(image_name):$(version)"

docker/star_ucsc_cufflinks/Dockerfile

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+FROM nciccbr/ccbr_ubuntu_base_20.04:v6
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install conda packages
+COPY environment.txt /data2/
+RUN mamba install -c conda-forge -c bioconda --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

docker/star_ucsc_cufflinks/environment.txt

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+cufflinks=2.2.1
+gffread
+sambamba=0.8.2
+samtools=1.16.1
+star=2.7.6a
+ucsc-bedgraphtobigwig
+ucsc-bedsort
+ucsc-gtftogenepred

docker/star_ucsc_cufflinks/meta.yml

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+dockerhub_namespace: nciccbr
+image_name: charlie_star_ucsc_cufflinks
+version: v0.1.0
+container: "$(dockerhub_namespace)/$(image_name):$(version)"