Ensure per product archival impacts hierarchy #12
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| name: testing_and_building_repo | |
| on: [push, pull_request] | |
| env: | |
| WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| name: Distribution Perl | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache conda | |
| id: minicondaCache | |
| uses: actions/cache@v3 | |
| with: | |
| path: $HOME/miniconda | |
| key: ${{ runner.os}}-build-miniconda | |
| - name: Cache cpanm external modules | |
| id: cpanmCache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/perl5ext | |
| key: ${{ runner.os}}-build-cpanm-external | |
| - name: Install libgd-dev and uuid-dev | |
| run: | | |
| sudo apt-get update | |
| # https://github.com/actions/runner-images/issues/2139 | |
| sudo apt-get remove -y nginx libgd3 | |
| sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl | |
| - name: Install baton and samtools | |
| run: | | |
| # 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 $HOME/miniconda/miniconda/samtools samtools | |
| env: | |
| WTSI_NPG_CONDA_REPO: https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic | |
| - name: Install cpanm | |
| run: | | |
| wget -qO - https://cpanmin.us | /usr/bin/perl - --sudo App::cpanminus | |
| - name: Install NPG Perl dependencies, and their CPAN dependencies | |
| run: | | |
| echo "$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_BUILD_BRANCH | |
| env: | |
| WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg | |
| - 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 | |
| - name: Archive CPAN logs on failure | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpan_log | |
| path: /home/runner/.cpanm/work/*/build.log | |
| retention-days: 5 |