all tabs gone #4
Workflow file for this run
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| name: CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - "*" | ||
| paths: | ||
| - data/** | ||
| # Allows you to run this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | ||
| permissions: | ||
| contents: write | ||
| pages: write | ||
| id-token: write | ||
| jobs: | ||
| # Placeholder | ||
| build-samples: | ||
| if: github.actor != 'github-actions[bot]' | ||
| runs-on: ubuntu-20.04 | ||
| environment: build | ||
| # needs: [build-drugs-beataml,depmap-docker-build] | ||
| steps: | ||
| - name: Checkout Repo | ||
| uses: actions/checkout@v2 | ||
| - name: Download artifacts from previous drug gen | ||
| uses: actions/download-artifact@v2 | ||
| - name: Pull sample image | ||
| run: docker pull sgosline/srp-samplechem | ||
| - name: Run sample-chem python command | ||
| run: | | ||
| docker run -v $PWD:/tmp sgosline/samplechem python build_script.py --samps | ||
| - name: List files cwd | ||
| run: ls -lah | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-2 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-2 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-2 | ||
| # path: additive-drugs-file-2 | ||
| # build-drugs-depmap-NCI60-pt1: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-drugs-depmap-CTRPv2-GDSC-gCSI-PRISM-CCLE-FIMM] | ||
| # steps: | ||
| # - name: Checkout Repo | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from previous drug gen | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-2 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # # - name: Install R | ||
| # # uses: r-lib/actions/setup-r@v2 | ||
| # # - name: Install R and Python Packages | ||
| # # run: | | ||
| # # Rscript build/depmap/requirements.r | ||
| # # pip install -r build/depmap/requirements.txt | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # - name: Run depmap NCI60 Drug retrieval | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: Rscript build/depmap/CreateDrugFileCL.R NCI60 | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-3 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-3 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-3 | ||
| # path: additive-drugs-file-3 | ||
| # build-drugs-depmap-NCI60-pt2: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-drugs-depmap-NCI60-pt1] | ||
| # steps: | ||
| # - name: Checkout Repo | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from previous drug gen | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-3 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # - name: Run depmap NCI60 Drug retrieval | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-4 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-4 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-4 | ||
| # path: additive-drugs-file-4 | ||
| # build-drugs-depmap-NCI60-pt3: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-drugs-depmap-NCI60-pt2] | ||
| # steps: | ||
| # - name: Checkout Repo | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from previous drug gen | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-4 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # - name: Run depmap NCI60 Drug retrieval | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-5 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-5 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-5 | ||
| # path: additive-drugs-file-5 | ||
| # build-drugs-depmap-NCI60-pt4: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-drugs-depmap-NCI60-pt3] | ||
| # steps: | ||
| # - name: Checkout Repo | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from previous drug gen | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-5 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # - name: Run depmap NCI60 Drug retrieval | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-6 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-6 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-6 | ||
| # path: additive-drugs-file-6 | ||
| # # build-drugs-depmap-NCI60-pt5: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt4] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-6 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-7 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-7 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-7 | ||
| # # path: additive-drugs-file-7 | ||
| # # build-drugs-depmap-NCI60-pt6: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt5] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-7 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-8 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-8 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-8 | ||
| # # path: additive-drugs-file-8 | ||
| # # build-drugs-depmap-NCI60-pt7: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt6] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-8 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-9 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-9 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-9 | ||
| # # path: additive-drugs-file-9 | ||
| # # build-drugs-depmap-NCI60-pt8: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt7] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-9 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-10 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-10 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-10 | ||
| # # path: additive-drugs-file-10 | ||
| # # build-drugs-depmap-NCI60-pt9: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt8] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-10 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-11 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-11 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-11 | ||
| # # path: additive-drugs-file-11 | ||
| # # build-drugs-depmap-NCI60-pt10: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt9] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-11 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-12 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-12 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-12 | ||
| # # path: additive-drugs-file-12 | ||
| # # build-drugs-depmap-NCI60-pt11: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # needs: [build-drugs-depmap-NCI60-pt10] | ||
| # # steps: | ||
| # # - name: Checkout Repo | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from previous drug gen | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-12 | ||
| # # - name: List files cwd | ||
| # # run: ls -lah | ||
| # # - name: Pull depmap image | ||
| # # run: docker pull jjacobson95/depmap | ||
| # # - name: Run depmap NCI60 Drug retrieval | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R NCI60 | ||
| # # - name: Copy drugs file to artifact | ||
| # # run: | | ||
| # # mkdir additive-drugs-file-13 | ||
| # # mv drugs.tsv ignore_chems.txt additive-drugs-file-13 | ||
| # # - name: Upload artifacts for genes | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: additive-drugs-file-13 | ||
| # # path: additive-drugs-file-13 | ||
| # build-drugs-depmap-capture-stragglers: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-drugs-depmap-NCI60-pt4] | ||
| # steps: | ||
| # - name: Checkout Repo | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from previous drug gen | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-6 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: List files cwd | ||
| # run: rm ignore_chems.txt | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # - name: Run depmap straggler Drug retrieval | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap Rscript /app/CreateDrugFileCL.R CTRPv2,GDSC,gCSI,PRISM,CCLE,FIMM,NCI60 | ||
| # - name: Copy drugs file to artifact | ||
| # run: | | ||
| # mkdir additive-drugs-file-7 | ||
| # mv drugs.tsv ignore_chems.txt additive-drugs-file-7 | ||
| # - name: Upload artifacts for genes | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-7 | ||
| # path: additive-drugs-file-7 | ||
| # build-cptac-samples: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-depmap-samples,cptac-docker-build] | ||
| # steps: | ||
| # #Add upload artifact from CPTAC Samples | ||
| # - name: Checkout CPTAC | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from depmap | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-samples | ||
| # - name: Download artifacts from DepMap (genes) | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: genes-file | ||
| # # - name: Copy DepMap sample from build location. | ||
| # # run: | | ||
| # # cp build/cptac/requirements.txt . | ||
| # # cp build/cptac/*.py . | ||
| # # # copy build/genes.csv . | ||
| # - name: Pull cptac image | ||
| # run: docker pull jjacobson95/cptac | ||
| # - name: Run CPTAC samples Container | ||
| # run: docker run -v $PWD:/tmp jjacobson95/cptac --geneFile=/tmp/genes.csv --prevSampleFile=/tmp/depmap_samples.csv | ||
| # - name: Copy file from CPTAC Samples Container | ||
| # run: | | ||
| # mkdir cptac-samples | ||
| # mv cptac_samples.csv cptac-samples | ||
| # - name: Upload artifacts for CPTAC | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: cptac-samples | ||
| # path: cptac-samples | ||
| # build-hcmi-samples: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-cptac-samples,hcmi-docker-build] | ||
| # steps: | ||
| # - name: Checkout HCMI | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from CPTAC | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-samples | ||
| # # - name: Build HCMI Image | ||
| # # run: docker build -t hcmi-samples-builder -f build/docker/Dockerfile.hcmi . | ||
| # - name: Pull hcmi image | ||
| # run: docker pull jjacobson95/hcmi | ||
| # - name: Run HCMI samples Container | ||
| # run: docker run -v $PWD:/tmp --name hcmi-samples-container jjacobson95/hcmi python 01-createHCMISamplesFile.py | ||
| # - name: Copy file from HCMI Samples Container | ||
| # run: | | ||
| # mkdir hcmi-samples | ||
| # for file in hcmi_samples.csv; do | ||
| # docker cp hcmi-samples-container:/usr/src/app/$file hcmi-samples/$file | ||
| # done | ||
| # - name: Get HCMI container logs | ||
| # run: docker logs hcmi-samples-container | ||
| # - name: Upload artifacts for HCMI | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: hcmi-samples | ||
| # path: hcmi-samples | ||
| # build-beataml-samples: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-hcmi-samples,beataml-docker-build] | ||
| # steps: | ||
| # #Add upload artifact from CPTAC Samples | ||
| # - name: Checkout BeatAML | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-samples | ||
| # - name: Pull beataml image | ||
| # run: docker pull jjacobson95/beataml | ||
| # - name: Run BeatAML Container with samples option | ||
| # run: docker run -v $PWD:/tmp --name beataml-samples-container jjacobson95/beataml python GetBeatAML.py --token ${{ secrets.SYNAPSE_TOKEN_SECRET }} --samples | ||
| # - name: Copy file from BeatAML Samples Container | ||
| # run: | | ||
| # mkdir beataml-samples | ||
| # for file in beataml_samples.csv; do | ||
| # docker cp beataml-samples-container:/usr/src/app/$file beataml-samples/$file | ||
| # done | ||
| # - name: Get BeatAML container logs | ||
| # run: docker logs beataml-samples-container | ||
| # - name: Upload artifacts for BeatAML | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: beataml-samples | ||
| # path: beataml-samples | ||
| # # Placeholder | ||
| # build-mpnst-samples: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # needs: [build-beataml-samples,mpnst-docker-build] | ||
| # steps: | ||
| # #Add upload artifact from CPTAC Samples | ||
| # - name: Checkout MPNST | ||
| # uses: actions/checkout@v2 | ||
| # build-hcmi: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-hcmi-samples] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout HCMI | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-samples | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # # - name: Build HCMI Image | ||
| # # run: docker build -t hcmi-builder -f build/docker/Dockerfile.hcmi . | ||
| # - name: Pull hcmi image | ||
| # run: docker pull jjacobson95/hcmi | ||
| # - name: Run HCMI Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp --name hcmi-container jjacobson95/hcmi /bin/bash -c "python 02-getHCMIData.py -m full_manifest.txt -t transcriptomics -o hcmi_transcriptomics.csv && python 02-getHCMIData.py -m full_manifest.txt -M full_manifest_files -t copy_number -o hcmi_copy_number.csv && python 02-getHCMIData.py -m full_manifest.txt -M full_manifest_files -t mutations -o hcmi_mutations.csv" | ||
| # - name: Copy files from HCMI Container | ||
| # run: | | ||
| # mkdir hcmi-files | ||
| # for file in hcmi_transcriptomics.csv hcmi_copy_number.csv hcmi_mutations.csv; do | ||
| # docker cp hcmi-container:/usr/src/app/$file hcmi-files/$file | ||
| # done | ||
| # cp hcmi_samples.csv hcmi-files | ||
| # - name: Get HCMI container logs | ||
| # run: docker logs hcmi-container | ||
| # - name: Upload artifacts for HCMI | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: hcmi-files | ||
| # path: hcmi-files | ||
| # check-hcmi-schema: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-hcmi] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code HCMI | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from HCMI Samples | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-samples | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-files | ||
| # - name: Download linkml | ||
| # run: | | ||
| # pip install linkml | ||
| # pip install linkml-validator | ||
| # - name: check dir | ||
| # run: ls | ||
| # - name: Run linkml schema checker | ||
| # run: bash schema/check_hcmi_linkml.sh | ||
| # build-beataml: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-beataml-samples,build-drugs-depmap-capture-stragglers] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code BeatAML | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from Beataml Samples | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-samples | ||
| # - name: Download artifacts from Drugs | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-7 | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Pull beataml image | ||
| # run: docker pull jjacobson95/beataml | ||
| # - name: Run BeatAML Container | ||
| # run: docker run -v $PWD:/tmp --name beataml-container jjacobson95/beataml python GetBeatAML.py --token ${{ secrets.SYNAPSE_TOKEN_SECRET }} | ||
| # - name: Copy files from BeatAML Container | ||
| # run: | | ||
| # mkdir beataml-files | ||
| # for file in beataml_transcriptomics.csv beataml_proteomics.csv beataml_mutations.csv beataml_drugs.tsv beataml_experiments.csv; do | ||
| # docker cp beataml-container:/usr/src/app/$file beataml-files/$file | ||
| # done | ||
| # cp beataml_samples.csv beataml-files | ||
| # - name: Get BeatAML container logs | ||
| # run: docker logs beataml-container | ||
| # - name: Upload artifact for BeatAML | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: beataml-files | ||
| # path: beataml-files | ||
| # check-beataml-schema: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-beataml] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code BeatAML | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from Beataml Samples | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-samples | ||
| # - name: Download artifacts from Beataml | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-files | ||
| # - name: Download linkml | ||
| # run: | | ||
| # pip install linkml | ||
| # pip install linkml-validator | ||
| # - name: check dir | ||
| # run: ls | ||
| # - name: Run linkml schema checker | ||
| # run: bash schema/check_beataml_linkml.sh | ||
| # # build-depmap: | ||
| # # if: github.actor != 'github-actions[bot]' | ||
| # # needs: [build-depmap-samples] | ||
| # # runs-on: ubuntu-20.04 | ||
| # # environment: build | ||
| # # steps: | ||
| # # - name: Checkout code DepMap | ||
| # # uses: actions/checkout@v2 | ||
| # # - name: List files cwd before | ||
| # # run: ls -lah | ||
| # # - name: Install coderdata | ||
| # # run: pip install coderdata | ||
| # # - name: Download depmap data from coder data | ||
| # # run: coderdata download --prefix depmap | ||
| # # - name: List files cwd after | ||
| # # run: ls -lah | ||
| # # - name: Copy files from DepMap Container | ||
| # # run: | | ||
| # # mkdir depmap-files | ||
| # # for file in *depmap*sv*; do | ||
| # # cp $file depmap-files/$file | ||
| # # done | ||
| # # - name: Upload artifact for DepMap | ||
| # # uses: actions/upload-artifact@v2 | ||
| # # with: | ||
| # # name: depmap-files | ||
| # # path: depmap-files | ||
| # build-depmap: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-depmap-samples,build-drugs-depmap-capture-stragglers] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout DepMap | ||
| # uses: actions/checkout@v2 | ||
| # # - name: Copy DepMap sample from build location. | ||
| # # run: | | ||
| # # cp build/depmap/requirements.txt . | ||
| # # cp build/depmap/requirements.r . | ||
| # # cp build/depmap/*.R . | ||
| # # cp build/depmap/*.py . | ||
| # # cp build/utils/* . | ||
| # - name: Download artifacts from DepMap (samples) | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-samples | ||
| # - name: Download artifacts from DepMap (genes) | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: genes-file | ||
| # - name: Download artifacts from Drugs | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: additive-drugs-file-7 | ||
| # - name: gzip drugs file | ||
| # run: gzip drugs.tsv | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: cat reqs | ||
| # run: cat requirements.txt | ||
| # - name: Pull depmap image | ||
| # run: docker pull jjacobson95/depmap | ||
| # # - name: docker save space and stats | ||
| # # run: | | ||
| # # docker image prune -f | ||
| # # docker container prune -f | ||
| # # docker volume prune -f | ||
| # # docker network prune -f | ||
| # # docker system df | ||
| # - name: Run depmap 02-pullDepMap.R Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp/ jjacobson95/depmap Rscript /app/02-pullDepMap.R /tmp/genes.csv /tmp/depmap_samples.csv | ||
| # - name: Run depmap 02b-pullSanger.R Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp/ jjacobson95/depmap Rscript /app/02b-pullSanger.R /tmp/genes.csv /tmp/depmap_samples.csv | ||
| # # - name: Run depmap 03-createDrugFile.RContainer | ||
| # # run: | | ||
| # # docker run -v $PWD:/tmp depmap Rscript 03-createDrugFile.R CTRPv2,GDSC,gCSI,PRISM,CCLE,FIMM,NCI60 | ||
| # - name: Run depmap 04-drug_dosage_and_curves.py Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp/ jjacobson95/depmap /opt/venv/bin/python /app/04-drug_dosage_and_curves.py --drugfile=/tmp/drugs.tsv.gz --curSampleFile=/tmp/depmap_samples.csv | ||
| # - name: Run depmap 01b-pullDrugs_LINCS.py Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap /opt/venv/bin/python /app/01b-pullDrugs_LINCS.py --drugFile /tmp/drugs.tsv.gz | ||
| # - name: Run depmap 04-pullDrugs_LINCS.py Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/depmap /opt/venv/bin/python /app/04-pullDrugs_LINCS.py --drugFile /tmp/drugs.tsv.gz | ||
| # - name: Run depmap 05-LINCS_perturbations.py Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp/ jjacobson95/depmap Rscript /app/05-LINCS_perturbations.R /tmp/genes.csv /tmp/drugs.tsv.gz /tmp/depmap_samples.csv | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Copy files from DepMap Container | ||
| # run: | | ||
| # mkdir depmap-files | ||
| # cp depmap_* depmap-files | ||
| # - name: Upload artifacts for DepMap | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: depmap-files | ||
| # path: depmap-files | ||
| # check-depmap-schema: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-depmap] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code DepMap | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from DepMap Samples | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-samples | ||
| # - name: Download artifacts from DepMap | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-files | ||
| # - name: Download linkml | ||
| # run: | | ||
| # pip install linkml | ||
| # pip install linkml-validator | ||
| # - name: check dir | ||
| # run: ls | ||
| # - name: Run linkml schema checker | ||
| # run: bash schema/check_depmap_linkml.sh | ||
| # build-cptac: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-cptac-samples] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout CPTAC | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from CPTAC | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-samples | ||
| # - name: Download artifacts from DepMap (genes) | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: genes-file | ||
| # - name: Copy files from build location. | ||
| # run: | | ||
| # cp build/cptac/*.py . | ||
| # cp build/cptac/requirements.txt . | ||
| # # copy build/genes.csv . | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Pull cptac image | ||
| # run: docker pull jjacobson95/cptac | ||
| # - name: Run CPTAC Container | ||
| # run: | | ||
| # docker run -v $PWD:/tmp jjacobson95/cptac --geneFile=/tmp/genes.csv --curSampleFile=/tmp/cptac_samples.csv | ||
| # - name: Copy files from CPTAC Container | ||
| # run: | | ||
| # mkdir cptac-files | ||
| # cp cptac_* cptac-files | ||
| # - name: Upload artifacts for CPTAC | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: cptac-files | ||
| # path: cptac-files | ||
| # check-cptac-schema: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-cptac] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code CPTAC | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from CPTAC Samples | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-samples | ||
| # - name: Download artifacts from CPTAC | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-files | ||
| # - name: Download linkml and gunzip files | ||
| # run: | | ||
| # pip install linkml | ||
| # pip install linkml-validator | ||
| # find . -type f -name '*.gz' -exec gunzip {} + | ||
| # - name: check dir | ||
| # run: ls | ||
| # - name: Run linkml schema checker | ||
| # run: bash schema/check_cptac_linkml.sh | ||
| # #placeholder | ||
| # build-mpnst: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-mpnst-samples] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code MPNST | ||
| # uses: actions/checkout@v2 | ||
| # # Placeholder | ||
| # check-mpnst-schema: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-mpnst] | ||
| # runs-on: ubuntu-20.04 | ||
| # environment: build | ||
| # steps: | ||
| # - name: Checkout code MPNST | ||
| # uses: actions/checkout@v2 | ||
| # # - name: Download artifacts from MPNST Samples | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: mpnst-samples | ||
| # # - name: Download artifacts from MPNST | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: mpnst-files | ||
| # # - name: Download linkml | ||
| # # run: | | ||
| # # pip install linkml | ||
| # # pip install linkml-validator | ||
| # # - name: check dir | ||
| # # run: ls | ||
| # # - name: Run linkml schema checker | ||
| # # run: bash schema/check_mpnst_linkml.sh | ||
| # data-visualization: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [check-hcmi-schema, check-beataml-schema, check-depmap-schema, check-cptac-schema, check-mpnst-schema] | ||
| # environment: build | ||
| # runs-on: ubuntu-20.04 | ||
| # steps: | ||
| # - name: Set up R | ||
| # uses: r-lib/actions/setup-r@v2 | ||
| # - name: Install R packages | ||
| # run: | | ||
| # R -e "install.packages('RColorBrewer', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('circlize', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('dplyr', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('readr', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('tools', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('ggplot2', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('reshape2', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # R -e "install.packages('ComplexUpset', dependencies=TRUE, repos='http://cran.rstudio.com/')" | ||
| # - name: checkout repo content | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-files | ||
| # - name: Download artifacts from BeatAML | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-files | ||
| # - name: Download artifacts from DepMap | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-files | ||
| # # - name: Download artifacts from MPNST | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: mpnst-files | ||
| # - name: Download artifacts from cptac | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-files | ||
| # # - name: Install coderdata and skip build steps | ||
| # # run: pip install coderdata | ||
| # # - name: Download cptac data from coder data | ||
| # # run: coderdata download --prefix cptac | ||
| # # - name: Download depmap data from coder data | ||
| # # run: coderdata download --prefix depmap | ||
| # # - name: Download all data from coder data | ||
| # # run: coderdata download | ||
| # - name: Create all-files directory | ||
| # run: mkdir all-files | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: List files dataSummary dir | ||
| # run: ls -lah dataSummary | ||
| # - name: Gzip all non-samples csv files in current dir. | ||
| # run: | | ||
| # find . -type f -name '*.csv' ! -name '*samples*' -exec gzip -k "{}" + | ||
| # - name: Run Visualization01 | ||
| # if: success() || failure() | ||
| # run: Rscript dataSummary/visualization01.R | ||
| # - name: Run Visualization02 | ||
| # if: success() || failure() | ||
| # run: Rscript dataSummary/visualization02.R | ||
| # - name: setup data-vis dir | ||
| # if: success() || failure() | ||
| # run: | | ||
| # mkdir -p data-vis | ||
| # rsync -av --remove-source-files --include='*.png' --include='*.pdf' --include='*table.csv' --exclude='*' . data-vis/ | ||
| # - name: Upload artifacts | ||
| # if: success() || failure() | ||
| # uses: actions/upload-artifact@v2 | ||
| # with: | ||
| # name: data-vis | ||
| # path: data-vis | ||
| # data-visualization-save-to-docs: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [data-visualization] | ||
| # environment: build | ||
| # runs-on: ubuntu-20.04 | ||
| # steps: | ||
| # - name: Checkout repo content | ||
| # uses: actions/checkout@v2 | ||
| # - name: Setup Git config and pull | ||
| # run: | | ||
| # git config user.name "jjacobson95" | ||
| # git config user.email "[email protected]" | ||
| # git pull | ||
| # - name: Download artifacts from data-vis | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: data-vis | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: List files .. | ||
| # run: ls -lah .. | ||
| # - name: List files all | ||
| # run: ls -lah * | ||
| # - name: Move files to docs directory | ||
| # run: | | ||
| # rsync -av --remove-source-files --include='*.png' --include='*.pdf' --exclude='*' . docs/assets/stats | ||
| # rsync -av --remove-source-files --include='*table.csv' --exclude='*' . docs/_data | ||
| # # rsync -av --remove-source-files --include='*.png' --include='*.pdf' --include='*table.csv' --exclude='*' . docs/ | ||
| # - name: List files in docs after moving | ||
| # run: ls -lah docs | ||
| # - name: List files in local after moving | ||
| # run: ls -lah | ||
| # - name: Git add and push new changes. | ||
| # run: | | ||
| # git add -f docs/* | ||
| # git status | ||
| # if git diff --staged --quiet; then | ||
| # echo "No changes to commit" | ||
| # else | ||
| # git commit -m "Add data visualization artifacts to docs" | ||
| # git push | ||
| # fi | ||
| # gen-stats-and-push: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [build-hcmi, build-beataml, build-depmap, build-cptac, build-mpnst] | ||
| # environment: build | ||
| # runs-on: ubuntu-20.04 | ||
| # steps: | ||
| # - name: Checkout repo content | ||
| # uses: actions/checkout@v2 | ||
| # - name: Setup Git config and pull | ||
| # run: | | ||
| # git config user.name "jjacobson95" | ||
| # git config user.email "[email protected]" | ||
| # git pull | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-files | ||
| # - name: Download artifacts from BeatAML | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-files | ||
| # - name: Download artifacts from DepMap | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-files | ||
| # # If this pipeline is supported in the future, Gen stats has been updated to include mpnst too. | ||
| # # - name: Download artifacts from MPNST | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: mpnst-files | ||
| # - name: Download artifacts from cptac | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-files | ||
| # - name: Install coderdata | ||
| # run: | | ||
| # pip install coderdata | ||
| # pip install pyyaml | ||
| # - name: Run stats generation script | ||
| # run: | | ||
| # python scripts/gen_stats.py | ||
| # - name: Git add and push new changes if they exist. | ||
| # run: | | ||
| # git pull | ||
| # mv stats.yml docs/_data/stats.yml | ||
| # git add -f docs/_data/stats.yml | ||
| # git status | ||
| # if git diff --staged --quiet; then | ||
| # echo "No changes to commit" | ||
| # else | ||
| # git commit -m "Add stats.yml to docs/_data" | ||
| # git push | ||
| # fi | ||
| # upload-to-figshare: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [check-hcmi-schema, check-beataml-schema, check-depmap-schema, check-cptac-schema, check-mpnst-schema] | ||
| # # needs: [build-hcmi, build-beataml, build-depmap, build-cptac, build-mpnst] | ||
| # environment: build | ||
| # runs-on: ubuntu-20.04 | ||
| # steps: | ||
| # - name: checkout repo content | ||
| # uses: actions/checkout@v2 | ||
| # - name: Download artifacts from HCMI | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: hcmi-files | ||
| # - name: Download artifacts from BeatAML | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: beataml-files | ||
| # - name: Download artifacts from CPTAC | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: cptac-files | ||
| # - name: Download artifacts from DepMap | ||
| # uses: actions/download-artifact@v2 | ||
| # with: | ||
| # name: depmap-files | ||
| # # - name: Download artifacts from MPNST | ||
| # # uses: actions/download-artifact@v2 | ||
| # # with: | ||
| # # name: mpnst-files | ||
| # - name: Create all-files directory | ||
| # run: mkdir all-files | ||
| # - name: List files cwd | ||
| # run: ls -lah | ||
| # - name: Move files to all-files | ||
| # run: | | ||
| # rsync -av --remove-source-files --include='*.csv' --include='*.tsv' --include='*.gz' --exclude='*' . all-files/ | ||
| # - name: gzip all files in all-files | ||
| # run: gzip all-files/* | ||
| # - name: gunzip all samples files in all-files | ||
| # run: gunzip all-files/*samples* | ||
| # - name: List files in all-files | ||
| # run: ls -lah all-files/ | ||
| # # - name: Upload to Figshare | ||
| # # # This can be updated to trigger with tag releases. | ||
| # # # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.event.release.tag_name }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} -p False | ||
| # # #This is a short term alternative. Links to branch. Not as pretty but okay for now. | ||
| # # #To do: Extract version number from setup.py and run there. This can occur after merge with package dev branch. | ||
| # # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.ref }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} --project_id 189342 --publish | ||
| # - name: Extract version from setup.py | ||
| # id: version | ||
| # run: echo "PACKAGE_VERSION=$(grep 'version=' setup.py | sed -n "s/.*version='\(.*\)'.*/\1/p")" >> $GITHUB_ENV | ||
| # - name: Upload to Figshare | ||
| # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ env.PACKAGE_VERSION }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} --project_id 189342 --publish | ||
| # - name: List files in all-files | ||
| # run: ls -lah all-files/ | ||
| # - name: Setup Git config | ||
| # run: | | ||
| # git config user.name "jjacobson95" | ||
| # git config user.email "[email protected]" | ||
| # - name: Commit and push changes | ||
| # run: | | ||
| # git pull | ||
| # mv figshare_latest.yml docs/_data | ||
| # git add -f docs/* | ||
| # git status | ||
| # git commit -m "Add figshare_latest.yml to docs/_data" | ||
| # git push | ||
| # update-package-download-function: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [upload-to-figshare] | ||
| # environment: build | ||
| # runs-on: ubuntu-20.04 | ||
| # steps: | ||
| # - name: checkout repo content | ||
| # uses: actions/checkout@v2 | ||
| # - name: Update figshare path in downloader.py | ||
| # run: | | ||
| # python scripts/update_download_function.py -y docs/_data/figshare_latest.yml -d coderdata/download/downloader.py | ||
| # cat coderdata/download/downloader.py | ||
| # - name: Setup Git config | ||
| # run: | | ||
| # git config user.name "jjacobson95" | ||
| # git config user.email "[email protected]" | ||
| # - name: Commit and push changes | ||
| # run: | | ||
| # git pull | ||
| # git add coderdata/download/downloader.py | ||
| # git commit -m "update downloader.py" | ||
| # git push | ||
| # run-tests: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [update-package-download-function] | ||
| # runs-on: ubuntu-latest | ||
| # strategy: | ||
| # fail-fast: false | ||
| # matrix: | ||
| # test-file: [ | ||
| # 'test_download_and_load_beataml.py', | ||
| # 'test_download_and_load_depmap.py', | ||
| # 'test_download_beataml_cli.py', | ||
| # 'test_download_depmap_cli.py', | ||
| # 'test_download_and_load_cptac.py', | ||
| # 'test_download_and_load_hcmi.py', | ||
| # 'test_download_cptac_cli.py', | ||
| # 'test_download_hcmi_cli.py', | ||
| # 'test_reformat_datasets.py', | ||
| # 'test_reload_one.py', | ||
| # 'test_reload_all.py', | ||
| # 'test_join_datasets.py', | ||
| # 'test_info.py' | ||
| # ] | ||
| # outputs: | ||
| # result: ${{ steps.test-outcome.outcome }} | ||
| # steps: | ||
| # - uses: actions/checkout@v2 | ||
| # with: | ||
| # fetch-depth: 0 | ||
| # - name: Set up Python | ||
| # uses: actions/setup-python@v2 | ||
| # with: | ||
| # python-version: '3.10' | ||
| # - name: Install dependencies | ||
| # run: | | ||
| # python -m pip install --upgrade pip | ||
| # pip install -r requirements.txt | ||
| # pip install pytest-xdist | ||
| # - name: Install as package | ||
| # run: | | ||
| # pip install . | ||
| # - name: Run test | ||
| # id: test-outcome | ||
| # run: | | ||
| # pytest -n 4 tests/${{ matrix.test-file }} | ||
| # build-and-publish: | ||
| # if: github.actor != 'github-actions[bot]' | ||
| # needs: [run-tests] | ||
| # runs-on: ubuntu-latest | ||
| # environment: build | ||
| # steps: | ||
| # - uses: actions/checkout@v2 | ||
| # with: | ||
| # fetch-depth: 0 | ||
| # - name: Fetch tags from main branch | ||
| # run: | | ||
| # git fetch origin 'refs/tags/*:refs/tags/*' | ||
| # - name: Set up Python | ||
| # uses: actions/setup-python@v2 | ||
| # with: | ||
| # python-version: '3.10' | ||
| # - name: Install dependencies | ||
| # run: | | ||
| # python -m pip install --upgrade pip | ||
| # pip install setuptools wheel twine packaging | ||
| # - name: Update version | ||
| # run: | | ||
| # # Extract the current version from setup.py | ||
| # CURRENT_VERSION=$(grep -oP "version='\K[0-9]+\.[0-9]+\.[0-9]+" setup.py) | ||
| # echo "Current version: $CURRENT_VERSION" | ||
| # # Fetch tags and get the latest tag, removing the 'v' prefix | ||
| # git fetch --tags | ||
| # LATEST_TAG=$(git describe --tags `git rev-list --tags --max-count=1` | sed 's/^v//') | ||
| # echo "Latest tag: $LATEST_TAG" | ||
| # # Use Python to compare versions | ||
| # HIGHER_VERSION=$(python -c "from packaging.version import parse as parse_version; \ | ||
| # current = parse_version('$CURRENT_VERSION'); \ | ||
| # latest = parse_version('$LATEST_TAG'); \ | ||
| # print(current if current > latest else latest)") | ||
| # echo "Higher version: $HIGHER_VERSION" | ||
| # # If current version is higher, increment patch version in setup.py | ||
| # if [ "$CURRENT_VERSION" == "$HIGHER_VERSION" ]; then | ||
| # IFS='.' read -r -a VERSION_PARTS <<< "$CURRENT_VERSION" | ||
| # PATCH=$((VERSION_PARTS[2] + 1)) | ||
| # NEW_VERSION="${VERSION_PARTS[0]}.${VERSION_PARTS[1]}.$PATCH" | ||
| # echo "Incremented version: $NEW_VERSION" | ||
| # sed -i "s/version='\([0-9]\+\.[0-9]\+\.\)[0-9]\+'/version='\1$PATCH'/" setup.py | ||
| # # Commit and push the updated setup.py | ||
| # git config --local user.email "[email protected]" | ||
| # git config --local user.name "GitHub Action" | ||
| # git pull | ||
| # git add setup.py | ||
| # git commit -m "Increment version number to $NEW_VERSION [skip ci]" | ||
| # git push | ||
| # else | ||
| # echo "No version increment needed" | ||
| # fi | ||
| # - name: Build local and publish to PyPI | ||
| # env: | ||
| # TWINE_USERNAME: __token__ | ||
| # TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN_SECRET }} | ||
| # run: | | ||
| # python setup.py sdist bdist_wheel | ||
| # twine upload dist/* --verbose | ||
