All Bactopia Tests #71
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| name: All Bactopia Tool Tests | |
| on: workflow_dispatch | |
| #schedule: | |
| # At 01:30 on Monday and Thursday | |
| #- cron: '30 1 * * 1,4' | |
| jobs: | |
| bactopia-tools-tests: | |
| runs-on: self-hosted | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout bactopia/bactopia | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ${{ github.run_id }}/bactopia | |
| - name: Setup ENV variables | |
| run: | | |
| echo "BACTOPIA_CI=/data/storage/bactopia-ci" >> $GITHUB_ENV | |
| echo "BACTOPIA_CONDA=/data/storage/bactopia-ci/envs/conda" >> $GITHUB_ENV | |
| echo "BACTOPIA_SINGULARITY=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV | |
| echo "BACTOPIA_TESTS=/data/storage/bactopia-ci/bactopia-tests/data" >> $GITHUB_ENV | |
| echo "BACTOPIA_WORKSPACE=${GITHUB_WORKSPACE}/${{ github.run_id }}/bactopia" >> $GITHUB_ENV | |
| echo "BACTOPIA_TMP=/data/storage/bactopia-tmp/${{ github.run_id }}" >> $GITHUB_ENV | |
| mkdir "/data/storage/bactopia-tmp/${{ github.run_id }}" | |
| chmod -R 777 "/data/storage/bactopia-tmp/${{ github.run_id }}" | |
| - name: Singularity Profile | |
| run: | | |
| source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh | |
| conda activate bactopia-ci | |
| cd ${{ env.BACTOPIA_WORKSPACE }} | |
| ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \ | |
| bash -c 'BACTOPIA_ARGS="-profile singularity --singularity_cache ${{ env.BACTOPIA_SINGULARITY }} --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
| pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}' | |
| - name: Docker Profile | |
| run: | | |
| source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh | |
| conda activate bactopia-ci | |
| cd ${{ env.BACTOPIA_WORKSPACE }} | |
| ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \ | |
| bash -c 'BACTOPIA_ARGS="-profile docker --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
| pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}' | |
| - name: Conda Profile | |
| run: | | |
| source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh | |
| conda activate bactopia-ci | |
| conda clean --all -y | |
| cd ${{ env.BACTOPIA_WORKSPACE }} | |
| ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \ | |
| bash -c 'BACTOPIA_ARGS="--is_ci --condadir ${{ env.BACTOPIA_CONDA }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
| pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}' | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-bactopia-tools | |
| path: | | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.out | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.err | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/.nextflow.log | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.log | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.err | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.out | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stderr.txt | |
| ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stdout.txt | |
| - name: Cleanup | |
| if: always() | |
| run: rm -rf ${GITHUB_WORKSPACE}/${{ github.run_id }} ${{ env.BACTOPIA_TMP }} |