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| c3996e4fae37a0ae01839cdd73752fb7b17e81bac2a8b39712463a7d518c4945 perlbrew.sh |
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| name: "Unit tests" | ||
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| on: [push, pull_request] | ||
|
|
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| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
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| defaults: | ||
| run: | ||
| shell: bash -l -e -o pipefail {0} | ||
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| 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 }} | ||
|
|
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| strategy: | ||
| matrix: | ||
| perl: ["5.26.3", "5.34.1"] | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - 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 ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib) | ||
| cpanm --quiet --notest Module::Build | ||
| cpanm --quiet --notest Alien::Tidyp | ||
| cpanm --quiet --notest Net::SSLeay | ||
| cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz | ||
| ./scripts/install_wsi_dependencies.sh "$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 |
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