add optional stage1 methods to allow analysis using product crams as input (instead of default BCL) #177
Workflow file for this run
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| name: testing_and_building_repo | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| name: Distribution Perl on ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # Caching cpanm external modules | |
| - name: Cache cpanm external modules | |
| id: cpanmCache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/perl5ext | |
| key: ${{ runner.os }}-build-cpanm-external | |
| - name: install cpanm | |
| run: | | |
| 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: | | |
| 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 | |
| WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF} | |
| - 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 --notest . | |
| - 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 | |
| # running ./Build dist and exporting files | |
| - name: run ./Build dist | |
| run: | | |
| eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext) | |
| export TEST_AUTHOR=1 | |
| ./Build dist | |
| export DIST_FILE=$(ls p4-*.tar.gz) | |
| export MD5_FILE=$DIST_FILE.md5 | |
| md5sum $DIST_FILE > $MD5_FILE | |
| export SHA256_FILE=$DIST_FILE.sha256 | |
| shasum -a 256 $DIST_FILE > $SHA256_FILE | |
| # 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 |