AVAMB snakemake - runs daily #389
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| # This workflow will install snakemake and AVAMB dependencies and run the AVAMB snakemake pipeline | |
| name: AVAMB snakemake - runs daily | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| schedule: | |
| - cron: "0 1 * * *" | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: '**/pyproject.toml' | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: '1.3.1-0' | |
| environment-file: workflow_avamb/envs/avamb.yaml | |
| environment-name: avamb | |
| create-args: >- | |
| python=3.9.16 | |
| init-shell: >- | |
| bash | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| - name: Install dependencies to avamb environment | |
| run: | | |
| which pip | |
| pip install -e . | |
| pip freeze | |
| git clone https://github.com/chklovski/CheckM2.git | |
| shell: micromamba-shell {0} | |
| - name: Install CheckM2 environment | |
| run: | | |
| micromamba create -n checkm2 python=3.8.15 pandas=2.1.1 | |
| micromamba env update -n checkm2 --file workflow_avamb/envs/checkm2.yml | |
| eval "$(micromamba shell hook --shell=bash)" | |
| micromamba activate checkm2 | |
| cd CheckM2 && git checkout e563159 && python setup.py install && cd .. | |
| checkm2 database --download | |
| shell: micromamba-shell {0} | |
| - name: Download fixtures | |
| run: | | |
| wget https://www.dropbox.com/scl/fi/q54wfho3ultb0otq5z3rh/testset_snakemake.zip\?rlkey\=7tbsc2giff0s42ppdmeb706fa\&dl\=0 -O testset_snakemake.zip | |
| unzip testset_snakemake.zip | |
| ls -la | |
| ls -la testset_snakemake | |
| pwd | |
| - name: Snakemake | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: '.test' | |
| snakefile: 'workflow_avamb/avamb.snake.conda.smk' | |
| args: '--cores 4 --configfile workflow_avamb/config.json --use-conda' |