Adding support for CGC w/ Automation

.dockerignore

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+.git/
+demo_scripts/
+docs/
+inst/
+man/
+

.github/workflows/cgc.yml

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+name: "Deploy to CGC"
+on:
+  release:
+    types: [released, edited]
+jobs:
+  cgc:
+    runs-on: ubuntu-20.04
+    name: "Deploy"
+    steps:
+      - uses: actions/checkout@v2
+      - id: cgcdeploy
+        uses: jordan-rash/[email protected]
+        with:
+          file_location: "cgc/netbid.cwl"
+          shortid: "stjude/netbid/netbid"
+        env: 
+          CGC_TOKEN: ${{ secrets.CGC_TOKEN }}
+

.github/workflows/publish.yml

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+name: Package
+on:
+  release:
+    types: [released, edited]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to GitHub Packages
+    runs-on: ubuntu-latest
+    steps:
+      - 
+        name: Check out the repo
+        uses: actions/checkout@v2
+      - 
+        name: Determine Short SHA
+        run: echo ${{ github.sha }} | tail -c 8 | (read; echo SHORT_SHA=$REPLY) >> $GITHUB_ENV
+      -
+        name: Sanitize Repo Name for Tagging
+        run: echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]' | (read; echo REPO_LOWER=$REPLY) >> $GITHUB_ENV
+      - 
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - 
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - 
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v1 
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.CLOUDY_USERNAME }}
+          password: ${{ secrets.CLOUDY_TOKEN }}
+      -
+        name: Login to Cancer Genomics Cloud Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: cgc-images.sbgenomics.com
+          username: ${{ secrets.CGC_USERNAME }}
+          password: ${{ secrets.CGC_TOKEN }}
+      - 
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile.cgc
+          push: true
+          tags: |
+            ghcr.io/${{ env.REPO_LOWER }}:latest
+            ghcr.io/${{ env.REPO_LOWER }}:${{ env.SHORT_SHA }}
+            ghcr.io/${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+            cgc-images.sbgenomics.com/${{ env.REPO_LOWER }}:latest
+            cgc-images.sbgenomics.com/${{ env.REPO_LOWER }}:${{ env.SHORT_SHA }}
+            cgc-images.sbgenomics.com/${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+          labels: |
+            org.opencontainers.image.source=https://github.com/${{ github.repository }} 
+      - 
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.gitignore

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 .Rhistory
 .RData
 .Ruserdata
+.DS_Store

Dockerfile.cgc

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+FROM r-base
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    libcurl4-gnutls-dev \
+    libxml2-dev \
+    libssl-dev \
+    libgit2-dev \
+    libcairo2-dev \
+    libxt-dev \
+    xvfb \
+    pandoc \ 
+    xauth \
+    xfonts-base \
+    libssl1.1 \ 
+    && rm -rf /var/lib/apt/lists/*
+
+# install R packages available in CRAN
+RUN R -e 'install.packages(c("optparse", "dplyr", "devtools", "BiocManager", "plot3D"))'
+
+# install R packages via Bioconductor
+RUN R -e 'BiocManager::install(c("biomaRt", "GSVA", "rhdf5", "ComplexHeatmap", "ConsensusClusterPlus", "DESeq2", "tximport", "impute", "limma", "GEOquery"))'
+
+# install NetBID2 from GitHub master branch
+RUN xvfb-run R -e 'devtools::install_github("jyyulab/NetBID", ref="master", dependencies="Depends")'
+
+WORKDIR /data
+COPY IBC_CCDI .
+
+ENTRYPOINT ["Rscript"]
+CMD ["IBC_CCDI.R"]
+#CMD ["-q", "-e", "packageVersion(\"NetBID2\")"]