fixed klebsiella recipe - pinned python and kaptive issue #200 #102
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| paths: | |
| - 'bohra/**' | |
| - '.github/workflows/CI.yml' | |
| - 'bohra/environments/**' | |
| - 'pyproject.toml' | |
| - 'environmet.yml' | |
| pull_request: | |
| branches: [ master ] | |
| paths: | |
| - 'bohra/**' | |
| - '.github/workflows/CI.yml' | |
| - 'bohra/environments/**' | |
| - 'pyproject.toml' | |
| - 'environment.yml' | |
| env: | |
| K2DB: "babykraken" | |
| K2DB_URL: "https://github.com/MDU-PHL/babykraken/raw/refs/heads/master/dist/babykraken.tar.gz" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| # this might remove tools that are actually needed, | |
| # if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| - name: Pull bohra | |
| uses: actions/checkout@v5 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: bohra | |
| environment-file: environment.yml | |
| auto-update-conda: true | |
| - name: Check disk usage | |
| run: df -h | |
| - name: Install Kraken2 database | |
| run: | | |
| wget ${K2DB_URL} | |
| tar zxvf ${K2DB}.tar.gz | |
| - name: Install bohra | |
| run: | | |
| pip3 install --no-deps . | |
| - name: Simple bohra test | |
| run: | | |
| bohra --version | |
| bohra --help | |
| bohra run --help | |
| - name: Install bohra deps | |
| run: | | |
| bohra deps install | |
| - name: Check bohra deps | |
| run: | | |
| bohra deps check | |
| - name: Big bohra test | |
| run: | | |
| export KRAKEN2_DEFAULT_DB="$PWD/$K2DB" | |
| bohra test --shovill_ram 8 --cpus 4 |