ci: update how we append to PATH in actions #4
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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: Install Dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libstdc++6 liblzma5 libbz2-1.0 bioperl perl | |
| - name: Set PATH for binaries | |
| run: | | |
| echo "PATH=$PWD/bin:$PWD/binaries/noarch:$PWD/binaries/linux:$GITHUB_PATH" >> $GITHUB_ENV | |
| - name: Check binaries | |
| run: | | |
| ! (ldd $PWD/binaries/linux/freebayes | grep 'not found') | |
| ! (ldd $PWD/binaries/linux/vcfuniq | grep 'not found') | |
| ! (ldd $PWD/binaries/linux/samtools | grep 'not found') | |
| ! (ldd $PWD/binaries/linux/bcftools | grep 'not found') | |
| # the check snippy step keeps erroring with /usr/bin/env: ‘perl’: Not a directory so check the perl installation | |
| - name: Check perl installation | |
| run: | | |
| perl --version | |
| which perl | |
| - name: Check snippy versions and configurations | |
| run: | | |
| snippy --version | |
| snippy --check | |
| snippy-core --version | |
| snippy-core --check | |
| - name: Run tests | |
| run: | | |
| make -C test | |