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|
name: Test release jar
on:
workflow_call:
inputs:
release_artifact:
required: true
type: string
jobs:
test-jar:
strategy:
fail-fast: true
matrix:
os: [ubuntu-latest,macos-11]
runs-on: ${{matrix.os}}
permissions:
contents: read
packages: write
steps:
- name: Checkout TestGenomicsDBJar
uses: actions/checkout@v3
with:
repository: GenomicsDB/TestGenomicsDBJar
ref: ml_genomicsdb_release
- name: Set version number
run: |
echo VERSION_NUMBER=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
echo GENOMICSDB_VERSION=${GITHUB_REF_NAME:1} >> $GITHUB_ENV
- uses: actions/setup-java@v3
with:
distribution: 'temurin'
java-version: '11'
- name: Download release artifacts
uses: actions/download-artifact@v3
with:
name: ${{ inputs.release_artifact }}
- name: Run smoke test
shell: bash
run: |
rm -f libtiledbgenomicsdb.*
mvn install:install-file -Dfile=genomicsdb-${VERSION_NUMBER}.jar \
-DgroupId=org.genomicsdb -DartifactId=genomicsdb -Dversion=${VERSION_NUMBER} \
-Dpackaging=jar -DpomFile=genomicsdb-${VERSION_NUMBER}.pom
./test_genomicsdbjar.sh
- name: Checkout GATK
uses: actions/checkout@v3
with:
repository: broadinstitute/gatk
lfs: 'true'
- name: Try GATK integration test
shell: bash
run: |
./gradlew installDist -Dgenomicsdb.version=${VERSION_NUMBER}
./gradlew test --tests *GenomicsDB*
|
