force cache #415
Workflow file for this run
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| name: unit-tests | |
| on: [push] | |
| env: | |
| spadesVer: 3.14.1 | |
| KRAKEN_DEFAULT_DB: /kraken-database | |
| # perl: [ '5.32', '5.30', '5.28' ] | |
| # perl: [ '5.32', '5.30.1', '5.16.3', '5.12.3' ] | |
| # os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] | |
| # https://github.com/marketplace/actions/setup-perl-environment | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-20.04' ] | |
| perl: [ '5.36.0' ] | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| name: Perl ${{ matrix.perl }} on ${{ matrix.os }} | |
| steps: | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| today=$(/bin/date -u '+%Y%m%d') | |
| echo $today | |
| echo "today=$today" >> $GITHUB_OUTPUT | |
| - name: set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| channel-priority: strict | |
| channels: conda-forge,bioconda,defaults | |
| mamba-version: "*" | |
| auto-activate-base: true | |
| activate-environment: "~/conda_pkgs_dir/my-env" | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| - name: conda info | |
| run: | | |
| conda info | |
| echo | |
| conda list | |
| echo | |
| conda config --show | |
| - name: Cache Conda env | |
| id: cache-conda | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/conda_pkgs_dir | |
| ~/.conda | |
| ~/.condarc | |
| #/usr/share/miniconda | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-perl_v${{ matrix.perl }}--${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 7 | |
| - name: conda installations | |
| shell: bash -el {0} | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| run: | | |
| mamba install -y perl shovill krona samclip flash mash seqtk \ | |
| kmc lighter megahit pilon trimmomatic perl-bioperl kraken=1 \ | |
| spades skesa=2.4 python=3.7 perl-cg-pipeline perl-gd blast prodigal \ | |
| perl-app-cpanminus perl-statistics-descriptive perl-config-simple \ | |
| perl-file-slurp perl-text-levenshtein perl-moo perl-list-moreutils kma=1.4 \ | |
| multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari | |
| - name: check installation | |
| shell: bash -el {0} | |
| run: | | |
| perl -v | |
| echo | |
| python -V | |
| echo | |
| which perl | |
| which python | |
| echo | |
| which kraken | |
| kraken --version | |
| which kraken-build | |
| echo | |
| echo conda | |
| conda info | |
| echo | |
| ls -l ~/conda_pkgs_dir /usr/share/miniconda || true | |
| - name: add some paths to PATH | |
| run: | | |
| echo "$GITHUB_WORKSPACE/CG-Pipeline/scripts" >> $GITHUB_PATH | |
| echo | |
| cat $GITHUB_PATH | |
| - name: checkout my repo | |
| uses: actions/checkout@v4 | |
| with: | |
| path: SneakerNet | |
| - name: checkout CG-Pipeline | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: lskatz/CG-Pipeline | |
| path: CG-Pipeline | |
| ref: v0.5 |