database dir for gene catalog #254
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: 1 | |
| 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 | |
| run-qc-and-assembly: | |
| runs-on: ubuntu-latest | |
| needs: build-and-dryrun | |
| 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 | |
| - name: cache example data | |
| id: get-data | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: test_reads.tar.gz | |
| key: example-data | |
| - name: Download test data | |
| if: steps.get-data.outputs.cache-hit != 'true' | |
| run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz | |
| - name: cache example data | |
| if: steps.get-data.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: test_reads.tar.gz | |
| key: ${{ steps.get-data.outputs.cache-primary-key }} | |
| - name: extract data | |
| run: | | |
| tar -xzf test_reads.tar.gz | |
| ls -l test_reads | |
| - name: get conda envs | |
| id: get-envs | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: $DATABASE_DIR/conda_envs | |
| key: assembly-conda-envs | |
| # - name: upack conda envs | |
| # if: steps.get-envs.outputs.cache-hit != 'true' | |
| # run: tar -xzf assembly_conda_envs.tar.gz | |
| - name: Init | |
| run: | | |
| atlas init "test_reads" --db-dir "$DATABASE_DIR" --threads "$N_THREADS" --working-dir wd | |
| - name: Install dependencies for qc and assembly | |
| if: steps.get-envs.outputs.cache-hit != 'true' | |
| run: atlas run assembly --conda-create-envs-only -w wd | |
| # - name: compress conda envs | |
| # run: | | |
| # tar -czf assembly_conda_envs.tar.gz $DATABASE_DIR/conda_envs | |
| - name: Cache conda envs | |
| if: steps.get-envs.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: $DATABASE_DIR/conda_envs | |
| key: ${{ steps.get-envs.outputs.cache-primary-key }} | |
| - name: Run QC | |
| run: | | |
| atlas run qc --resources mem=$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/Sample1/logs | |
| - name: Cache working dir | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: wd | |
| key: assembly-working-dir | |
| run-genecatalog: | |
| runs-on: ubuntu-latest | |
| needs: run-qc-and-assembly | |
| 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 | |
| - name: get conda envs | |
| id: get-genecatalog-envs | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: $DATABASE_DIR/conda_envs | |
| key: binning-conda-envs | |
| restore-keys: | | |
| assembly-conda-envs | |
| - name: Restore working dir | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: wd | |
| key: assembly-working-dir | |
| - name: dryrun assembly shold need nothing to be done | |
| run: | | |
| ls -l wd | |
| atlas run assembly -n | |
| - name: Test Genecatalog | |
| run: | | |
| atlas run genecatalog --resources mem=$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/Sample1/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/Sample1/logs |