Update docker-build.yml #3
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | ||
