Allow for GT to be a nocall if GQ and PL[0] are zero instead of homre… #156
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 |