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Add workflow Ensembl/ensembl-production
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| name: Ensembl/ensembl-production | ||
| on: | ||
| push: | ||
| branches: | ||
| - "**/*" | ||
| pull_request: | ||
| schedule: [] | ||
| concurrency: | ||
| # # This item has no matching transformer | ||
| # maximum_number_of_builds: 0 | ||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/checkout@v4.1.0 | ||
| - uses: shogo82148/actions-setup-perl@v1.27.0 | ||
| with: | ||
| perl-version: "${{ matrix.perl }}" | ||
| - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | ||
| - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | ||
| - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | ||
| - run: export ENSEMBL_BRANCH=master | ||
| - run: export SECONDARY_BRANCH=main | ||
| - run: echo "TRAVIS_BRANCH=${{ github.ref }}" | ||
| - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | ||
| - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | ||
| - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | ||
| - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | ||
| - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | ||
| - run: cd htslib | ||
| - run: make | ||
| - run: export HTSLIB_DIR=$(pwd -P) | ||
| - run: cd .. | ||
| - run: cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile . | ||
| - run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile . | ||
| - run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile . | ||
| - run: export PERL5LIB=$PERL5LIB:$PWD/bioperl-live | ||
| - run: cpanm --sudo -v --installdeps --notest . | ||
| - run: cpanm --sudo -n Devel::Cover::Report::Coveralls | ||
| - run: cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf | ||
| - run: mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"' | ||
| - run: "./travisci/harness.sh" | ||
| # # This item has no matching transformer | ||
| # - email: | ||
| # on_success: always | ||
| # on_failure: always | ||
| - uses: rtCamp/action-slack-notify@v2.2.1 | ||
| env: | ||
| SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | ||
| strategy: | ||
| matrix: | ||
| perl: | ||
| - '5.14' | ||
| - 5.26.2 | ||
| include: | ||
| - COVERALLS: 'true' | ||
| DB: mysql | ||
| services: | ||
| mysql: | ||
| image: mysql | ||
| env: | ||
| COVERALLS: "${{ matrix.COVERALLS }}" | ||
| DB: "${{ matrix.DB }}" | ||
| test_2: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| COVERALLS: 'true' | ||
| DB: mysql | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/checkout@v4.1.0 | ||
| - uses: actions/setup-python@v5.0.0 | ||
| with: | ||
| python-version: 3.7.6 | ||
| - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | ||
| - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | ||
| - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | ||
| - run: export ENSEMBL_BRANCH=master | ||
| - run: export SECONDARY_BRANCH=main | ||
| - run: echo "TRAVIS_BRANCH=${{ github.ref }}" | ||
| - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | ||
| - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | ||
| - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | ||
| - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | ||
| - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | ||
| - run: cd htslib | ||
| - run: make | ||
| - run: export HTSLIB_DIR=$(pwd -P) | ||
| - run: cd .. | ||
| - run: pip install -r requirements-test.txt | ||
| - run: pip install -e . | ||
| - run: pytest src/python/test | ||
| # # This item has no matching transformer | ||
| # - email: | ||
| # on_success: always | ||
| # on_failure: always | ||
| - uses: rtCamp/action-slack-notify@v2.2.1 | ||
| env: | ||
| SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | ||
| services: | ||
| mysql: | ||
| image: mysql | ||
| test_3: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| COVERALLS: 'true' | ||
| DB: mysql | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/checkout@v4.1.0 | ||
| - uses: actions/setup-python@v5.0.0 | ||
| with: | ||
| python-version: 3.8 | ||
| - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | ||
| - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | ||
| - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | ||
| - run: export ENSEMBL_BRANCH=master | ||
| - run: export SECONDARY_BRANCH=main | ||
| - run: echo "TRAVIS_BRANCH=${{ github.ref }}" | ||
| - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | ||
| - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | ||
| - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | ||
| - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | ||
| - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | ||
| - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | ||
| - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | ||
| - run: cd htslib | ||
| - run: make | ||
| - run: export HTSLIB_DIR=$(pwd -P) | ||
| - run: cd .. | ||
| - run: pip install -r requirements-test.txt | ||
| - run: pip install -e . | ||
| - run: pytest src/python/test | ||
| # # This item has no matching transformer | ||
| # - email: | ||
| # on_success: always | ||
| # on_failure: always | ||
| - uses: rtCamp/action-slack-notify@v2.2.1 | ||
| env: | ||
| SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | ||
| services: | ||
| mysql: | ||
| image: mysql |