Archive Illumina samplesheet if present #154
Workflow file for this run
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| name: "Unit tests" | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l -e -o pipefail {0} | |
| env: | |
| PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached | |
| NPG_LIB: ~/perl5npg # NPG modules installed here, not cached | |
| WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic" | |
| CONDA_TEST_ENV: test-environment | |
| WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg | |
| WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }} | |
| strategy: | |
| matrix: | |
| perl: ["5.26.3", "5.34.1"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: "Install OS dependencies" | |
| 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: "Initialize Miniconda" | |
| run: | | |
| echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile" | |
| - name: "Install Conda packages" | |
| run: | | |
| conda config --prepend pkgs_dirs ~/conda/pkgs | |
| conda config --prepend envs_dirs ~/conda/envs | |
| conda config --set auto_update_conda False | |
| conda config --prepend channels "$WSI_CONDA_CHANNEL" | |
| conda info | |
| conda create -y -n "$CONDA_TEST_ENV" | |
| conda install -y -n "$CONDA_TEST_ENV" baton | |
| conda install -y -n "$CONDA_TEST_ENV" samtools | |
| - name: "Cache Perl" | |
| id: cache-perl | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.PERL_CACHE }} | |
| key: ${{ runner.os }}-${{ matrix.perl }}-perl | |
| - name: "Install Perlbrew" | |
| if: steps.cache-perl.outputs.cache-hit != 'true' | |
| run: | | |
| curl -sSL https://install.perlbrew.pl -o perlbrew.sh | |
| sha256sum -c .github/workflows/perlbrew.sha256 | |
| export PERLBREW_ROOT=${{ env.PERL_CACHE }} | |
| sh perlbrew.sh | |
| source ${{ env.PERL_CACHE }}/etc/bashrc | |
| perlbrew available | |
| perlbrew install --notest perl-${{ matrix.perl }} | |
| perlbrew use perl-${{ matrix.perl }} | |
| perlbrew install-cpanm | |
| - name: "Initialize Perlbrew" | |
| run: | | |
| echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile" | |
| - name: "Install Perl dependencies" | |
| run: | | |
| cpanm --local-lib=${{ env.PERL_CACHE }} local::lib | |
| eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB") | |
| eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib) | |
| cpanm --quiet --notest Module::Build | |
| cpanm --quiet --notest Net::SSLeay | |
| cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz | |
| ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \ | |
| perl-dnap-utilities \ | |
| perl-irods-wrap \ | |
| ml_warehouse \ | |
| npg_tracking \ | |
| npg_seq_common \ | |
| npg_qc \ | |
| npg_irods | |
| cpanm --installdeps --notest . | |
| - name: "Log install failure" | |
| if: ${{ failure() }} | |
| run: | | |
| find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20 {} \; | |
| - name: "Archive CPAN logs on failure" | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: cpan_log | |
| path: ~/.cpanm/work/*/build.log | |
| retention-days: 5 | |
| - name: "Run tests" | |
| run: | | |
| conda activate "$CONDA_TEST_ENV" | |
| conda info --envs | |
| eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib) | |
| eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB") | |
| export TEST_AUTHOR=1 | |
| perl Build.PL | |
| ./Build test --verbose | |
| ./Build install |