testing_and_building_repo.yml

name: testing_and_building_repo
on: [push, pull_request]
jobs:
  build: 
    strategy:
      matrix:
        os: ['ubuntu-18.04']
        
    runs-on: ${{matrix.os}} 
    name: Distribution Perl on ${{ matrix.os }} 
    steps:
    - uses: actions/checkout@v2 
    
    # Caching conda
    - name: Cache conda
      id: minicondaCache
      uses: actions/cache@v2
      with:
        path: $HOME/miniconda
        key: ${{ matrix.os}}-build-miniconda
    
   # Caching cpanm external modules
    - name: Cache cpanm external modules
      id: cpanmCache
      uses: actions/cache@v2
      with:
        path: ~/perl5ext  
        key: ${{ matrix.os}}-build-cpanm-external
 
    #install libgd-dev and uuid-dev
    - name: install libgd-dev and uuid-dev 
      run:
          sudo apt-get install -y libgd-dev uuid-dev 
      
    - name: install conda client, baton,samtools
      if: steps.minicondaCache.outputs.cache-hit != 'true' # if no cache for conda found
      run: |
          wget "https://repo.continuum.io/miniconda/Miniconda2-4.6.14-Linux-x86_64.sh" -O miniconda.sh;
          chmod +x miniconda.sh;
          ./miniconda.sh -b  -p $HOME/miniconda;
          export PATH=$HOME/miniconda/bin:$PATH;
 
          # install baton from our conda channel
          conda install --yes --channel ${WTSI_NPG_CONDA_REPO} --channel default --mkdir --prefix $HOME/miniconda/miniconda/baton baton;
 
          # install samtools from our conda channel
          # this is needed for our basic IRODS Perl wrapper to work
          conda install --yes --channel ${WTSI_NPG_CONDA_REPO} --channel default --mkdir --prefix $HOME/miniconda/miniconda/samtools samtools
      env:  
        WTSI_NPG_CONDA_REPO: https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic
  
    - name: install cpanm 
      run: |
          #installing cpanm
          wget -qO - https://cpanmin.us | /usr/bin/perl - --sudo App::cpanminus

    #run the perl install script
    - name: install NPG Perl dependencies, and their CPAN dependencies
      run: |
          echo "$HOME/miniconda/samtools/bin" >> $GITHUB_PATH
          cpanm --local-lib=~/perl5ext local::lib && eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib)
          ${GITHUB_WORKSPACE}/scripts/install_npg_perl_dependencies.sh $WTSI_NPG_GITHUB_URL $WTSI_NPG_CONDA_REPO $WTSI_NPG_BUILD_BRANCH
      env:
        WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
        WTSI_NPG_CONDA_REPO: https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic
        WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF} #getting name of current github branch
      
    - name: install cpanm dependencies
      run: |
          eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5npg)
          eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext)
          cpanm --installdeps .

    - name: run Build.PL and ./Build   
      run: |
          eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext)
          eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5npg)
          export TEST_AUTHOR=1
          perl Build.PL && ./Build test --verbose && ./Build install

    # Archive logs if failure
    - name: Archive CPAN logs
      if: ${{ failure() }}
      uses: actions/upload-artifact@v2
      with:
        name: cpan_log
        path: /home/runner/.cpanm/work/*/build.log
        retention-days: 5