main.yml

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