Migrate CI workflow from apt-get to conda/miniforge #35
Workflow file for this run
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: snippy-env | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| - name: Install Dependencies | |
| shell: bash -el {0} | |
| run: | | |
| conda install -y \ | |
| samtools bcftools freebayes bedtools \ | |
| bwa minimap2 parallel vcflib vt snpeff \ | |
| seqtk snp-sites wgsim any2fasta \ | |
| perl-bioperl samclip | |
| - name: Add binaries to PATH | |
| shell: bash -el {0} | |
| run: | | |
| echo "$PWD/bin:$PWD/binaries/noarch:$PWD/binaries/linux" >> $GITHUB_PATH | |
| - name: Check snippy versions and configurations | |
| shell: bash -el {0} | |
| run: | | |
| snippy --version | |
| snippy --check | |
| snippy-core --version | |
| snippy-core --check | |
| - name: Run tests | |
| shell: bash -el {0} | |
| run: | | |
| make -C test | |