init atlas for #246
Workflow file for this run
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| name: Combined Workflow | |
| on: [push] | |
| defaults: | |
| run: | |
| shell: bash -el {0} # use default shell | |
| jobs: | |
| build-and-dryrun: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 2 | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| # - name: Get current month | |
| # id: date | |
| # run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}" | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| # persist on the same month. | |
| cache-environment-key: atlasenv- #${{ steps.date.outputs.date }} | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| - name: Test atlas | |
| run: | | |
| atlas --help | |
| atlas --version | |
| - name: test import modules atlas | |
| run: | | |
| python -c "from atlas import utils" | |
| - name: Dryrun | |
| run: test/dryrun.sh | |
| - name: Test init many samples | |
| run: ./test/test_init_many_samples.sh | |
| test-qc: | |
| runs-on: ubuntu-latest | |
| needs: build-and-dryrun | |
| strategy: | |
| max-parallel: 1 | |
| env: | |
| N_THREADS: 2 | |
| MEM: 3 | |
| DATABASE_DIR: databases | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| qc_and_assembly: | |
| runs-on: ubuntu-latest | |
| env: | |
| N_THREADS: 2 | |
| MEM: 3 | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| - name: Download test data | |
| run: | | |
| wget https://zenodo.org/record/3992790/files/test_reads.tar.gz | |
| tar -xzf test_reads.tar.gz | |
| - name: get conda envs | |
| id: get-envs | |
| uses: actions/cache@v2 | |
| with: | |
| path: databases/conda_envs | |
| key: assembly-conda-envs | |
| # - name: upack conda envs | |
| # if: steps.get-enfs.outputs.cache-hit != 'true' | |
| # run: tar -xzf assembly_conda_envs.tar.gz | |
| - name: Init | |
| run: | | |
| atlas init "example_data/reads/test" --db-dir "$DATABASE_DIR" --threads "$N_THREADS" --working-dir wd | |
| - name: Install dependencies for assembly | |
| if: steps.get-enfs.outputs.cache-hit != 'true' | |
| run: atlas run assembly --conda-create-envs-only | |
| # - name: compress conda envs | |
| # run: | | |
| # tar -czf assembly_conda_envs.tar.gz $DATABASE_DIR/conda_envs | |
| - name: Cache conda envs | |
| if: steps.get-enfs.outputs.cache-hit != 'true' | |
| uses: actions/cache@v2 | |
| env: | |
| cache-name: assembly-conda-envs | |
| with: | |
| path: databases/conda_envs | |
| key: assembly-conda-envs | |
| - name: Run QC | |
| run: | | |
| atlas run qc --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd | |
| - name: Test Assembly | |
| run: | | |
| atlas run assembly --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd | |
| - name: Store Logs | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs | |
| path: wd/logs | |
| - name: Store Sample Logs | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: sample_logs | |
| path: wd/Streptococcus/logs | |
| full-test: | |
| runs-on: ubuntu-latest | |
| needs: build-and-dryrun | |
| strategy: | |
| max-parallel: 1 | |
| env: | |
| N_THREADS: 2 | |
| MEM: 3 | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| # - name: Clone Example Data Repository | |
| # run: git clone https://github.com/metagenome-atlas/example_data.git | |
| - name: Run Test | |
| run: | | |
| test/test_ci.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 | |
| - name: Store Logs | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs | |
| path: test_ci/logs | |
| - name: Store Sample Logs | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: sample_logs | |
| path: test_ci/Streptococcus/logs |