Allow for GT to be a nocall if GQ and PL[0] are zero instead of homre… #157
Workflow file for this run
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| name: Release | |
| on: | |
| push: | |
| tags: | |
| - v* | |
| env: | |
| PREREQS_ENV: ${{github.workspace}}/prereqs.sh | |
| PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs | |
| PROTOBUF_VERSION: 3.19.4 | |
| CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install | |
| GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build | |
| BUILD_DISTRIBUTABLE_LIBRARY: true | |
| jobs: | |
| build-and-push-mac-dylib: | |
| runs-on: macos-12 | |
| outputs: | |
| tag_message: ${{env.TAG_MESSAGE}} | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-package: jdk | |
| java-version: '17' | |
| - name: Set version number | |
| run: echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV | |
| - name: Set tag messsage | |
| run: | | |
| git fetch --tags --force | |
| echo "TAG_MESSAGE=$(git tag -l --sort=-taggerdate --format='%(contents)' $(git describe --tags $(git branch --show-current) ))" >> $GITHUB_ENV | |
| - name: Install Prerequisites | |
| shell: bash | |
| working-directory: ${{github.workspace}}/scripts/prereqs | |
| run: | | |
| echo "Installing Prerequistes for MacOS..." | |
| export INSTALL_PREFIX=$PREREQS_INSTALL_DIR | |
| BUILD_DISTRIBUTABLE_LIBRARY=true ./install_prereqs.sh | |
| - name: Build GenomicsDB distributable | |
| shell: bash | |
| run: | | |
| echo "Building GenomicsDB for MacOS..." | |
| export INSTALL_PREFIX=$PREREQS_INSTALL_DIR | |
| mkdir -p $GENOMICSDB_BUILD_DIR | |
| source $PREREQS_ENV | |
| cmake $GITHUB_WORKSPACE \ | |
| -DCMAKE_OSX_ARCHITECTURES="arm64;x86_64" \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \ | |
| -DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR \ | |
| -DGENOMICSDB_PROTOBUF_VERSION=$PROTOBUF_VERSION \ | |
| -DGENOMICSDB_RELEASE_VERSION=${VERSION_NUMBER} \ | |
| -DBUILD_JAVA=1 -DUSE_HDFS=0 -DBUILD_DISTRIBUTABLE_LIBRARY=1 | |
| make -j4 | |
| make install | |
| cp $CMAKE_INSTALL_PREFIX/lib/libtiledbgenomicsdb.dylib . | |
| - name: Archive libraries as artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: libtiledbgenomicsdb.dylib.${{ github.ref_name }} | |
| path: libtiledbgenomicsdb.dylib | |
| release-jar: | |
| needs: [build-and-push-mac-dylib] | |
| uses: ./.github/workflows/release_jar.yml | |
| with: | |
| dylib_artifact: libtiledbgenomicsdb.dylib.${{ github.ref_name }} | |
| test: | |
| needs: [build-and-push-mac-dylib, release-jar] | |
| uses: ./.github/workflows/release_test.yml | |
| with: | |
| release_artifact: release.${{ github.ref_name }} | |
| tag_message: ${{ needs.build-and-push-mac-dylib.outputs.tag_message }} | |
| publish: | |
| needs: [test] | |
| uses: ./.github/workflows/release_publish.yml | |
| with: | |
| release_artifact: release.${{ github.ref_name }} | |
| secrets: inherit |