From f862d441b61cb249f6eb431462b9827d5cfa7b33 Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Fri, 12 Feb 2021 13:32:36 -0500 Subject: [PATCH] disable singularity from CI --- .github/workflows/pipeline.yaml | 122 ++++++++++++++++---------------- 1 file changed, 61 insertions(+), 61 deletions(-) diff --git a/.github/workflows/pipeline.yaml b/.github/workflows/pipeline.yaml index 98bea48eb..958f4ed5d 100644 --- a/.github/workflows/pipeline.yaml +++ b/.github/workflows/pipeline.yaml @@ -92,67 +92,67 @@ jobs: # name: conda-logs # path: workflow/logs/ #----------------------------------------------------------------------------# - pipeline_singularity: - name: Pipeline with Singularity - runs-on: ubuntu-latest - strategy: - fail-fast: false - timeout-minutes: 60 - steps: - #------------------------------------------------------------------------# - - name: setup environment variables - run: | - echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV - echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV - echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV - echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV - #------------------------------------------------------------------------# - # Checkout Repository - - name: checkout repo - uses: actions/checkout@v2 - # Clean results - - name: clean results - run: | - rm -rf results/iqtree/ results/metadata results/multiqc; - #------------------------------------------------------------------------# - # Setup singularity - - name: setup singularity - uses: eWaterCycle/setup-singularity@v5 - with: - singularity-version: 3.6.3 - #------------------------------------------------------------------------# - # pull container - - name: pull container - run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev - #------------------------------------------------------------------------# - # Configure sra-toolkit - - name: configure sra-toolkit - run: | - mkdir -p ~/.ncbi/; - printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg; - # run help - - name: run help - run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions help; - # run all - - name: run all - run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions all; - # run report - - name: run report - shell: bash -l {0} - run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions --report workflow/report/report.html all; - #------------------------------------------------------------------------# - # Artifact Upload - - name: artifact singularity-report - uses: actions/upload-artifact@v2 - with: - name: singularity-report - path: workflow/report/report.html - # - name: artifact singularity-logs - # uses: actions/upload-artifact@v2 - # if: always() - # with: - # name: singularity-logs - # path: workflow/logs/ + # pipeline_singularity: + # name: Pipeline with Singularity + # runs-on: ubuntu-latest + # strategy: + # fail-fast: false + # timeout-minutes: 60 + # steps: + # #------------------------------------------------------------------------# + # - name: setup environment variables + # run: | + # echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV + # echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV + # echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV + # echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV + # #------------------------------------------------------------------------# + # # Checkout Repository + # - name: checkout repo + # uses: actions/checkout@v2 + # # Clean results + # - name: clean results + # run: | + # rm -rf results/iqtree/ results/metadata results/multiqc; + # #------------------------------------------------------------------------# + # # Setup singularity + # - name: setup singularity + # uses: eWaterCycle/setup-singularity@v5 + # with: + # singularity-version: 3.6.3 + # #------------------------------------------------------------------------# + # # pull container + # - name: pull container + # run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev + # #------------------------------------------------------------------------# + # # Configure sra-toolkit + # - name: configure sra-toolkit + # run: | + # mkdir -p ~/.ncbi/; + # printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg; + # # run help + # - name: run help + # run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions help; + # # run all + # - name: run all + # run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions all; + # # run report + # - name: run report + # shell: bash -l {0} + # run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions --report workflow/report/report.html all; + # #------------------------------------------------------------------------# + # # Artifact Upload + # - name: artifact singularity-report + # uses: actions/upload-artifact@v2 + # with: + # name: singularity-report + # path: workflow/report/report.html + # # - name: artifact singularity-logs + # # uses: actions/upload-artifact@v2 + # # if: always() + # # with: + # # name: singularity-logs + # # path: workflow/logs/ #----------------------------------------------------------------------------# pipeline_docker: name: Pipeline with Docker