stable-apptainer #8
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| name: stable-apptainer | |
| on: | |
| schedule: | |
| - cron: "15 0 * * 1" | |
| workflow_dispatch: | |
| # env: | |
| # COMPAREM2_PROFILE: "profile/conda/default" | |
| jobs: | |
| create-env: | |
| name: ${{ matrix.os }} | |
| runs-on: self-hosted | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v2 | |
| - name: create environment with mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "<2" | |
| miniforge-version: "latest" | |
| channels: conda-forge,bioconda | |
| auto-activate-base: false | |
| channel-priority: true | |
| activate-environment: comparem2_stable | |
| environment-file: resources/env_stable.yaml | |
| - name: check solution | |
| run: | | |
| mamba env export | |
| - name: test installation | |
| run: | | |
| python --version | |
| snakemake --version | |
| apptainer --version | |
| which comparem2 | |
| comparem2 --help | |
| comparem2 --version | |
| comparem2 --cite | |
| comparem2 --status | |
| - name: fast | |
| run: | | |
| unzip tests/E._faecium/fna.zip | |
| comparem2 --config input_genomes="*.fna" --until fast | |
| tree results_comparem2 | |
| rm -rf .snakemake results_comparem2 *.fna | |
| - name: full | |
| run: | | |
| unzip tests/E._faecium/fna.zip | |
| comparem2 --config input_genomes="*.fna" --omit-from antismash | |
| tree results_comparem2 | |
| rm -rf .snakemake results_comparem2 *.fna | |
| - name: dry run # With apptainer, dry run can't run without the image being pulled, so the dry run comes in the end instead. | |
| run: | | |
| comparem2 --dry-run | |
| rm -rf .snakemake results_comparem2 | |
| comparem2 --until metadata | |
| rm -rf .snakemake results_comparem2 | |
| touch dummy_1.fa; comparem2 --dry-run | |
| touch dummy_2.fa; comparem2 --dry-run | |
| touch dummy_3.fa; comparem2 --dry-run | |
| unzip tests/E._faecium/fna.zip | |
| comparem2 --config input_genomes="*.fna" --dry-run | |
| comparem2 --config input_genomes="*.fna" --until fast --dry-run | |
| comparem2 --config input_genomes="*.fna" --until isolate --dry-run | |
| comparem2 --config input_genomes="*.fna" --until meta --dry-run | |
| comparem2 --config input_genomes="*.fna" --until downloads --dry-run | |
| ls dummy_{2,3}.fa > fofn.txt; comparem2 --config fofn="fofn.txt" --dry-run | |
| rm -rf .snakemake results_comparem2 *.fna | |
| # Runner can be started from thylakoid@johans: | |
| # sudo -u ci-runner bash | |
| # cd /mnt/evo/actions-runner/ | |
| # ./run.sh |