|
| 1 | +name: Build and Upload Genome Nexus Annotator |
| 2 | + |
| 3 | +on: |
| 4 | + push: |
| 5 | + paths: |
| 6 | + - '.github/workflows/build_genome_nexus_annotator.yml' |
| 7 | + |
| 8 | +env: |
| 9 | + # versions for dependencies used in annotator.jar build |
| 10 | + MAVEN_VERSION: '3.9.9' |
| 11 | + COMMIT_HASH: "2e67ebd08cf7c26bf1f55f2baf4b73ac36531119" |
| 12 | + JAVA_VERSION: "21" |
| 13 | + JAVA_DISTRIBUTION: "corretto" |
| 14 | + # synapse id of the Genome Nexus Testing folder |
| 15 | + OUTPUT_FOLDER_SYNAPSE_ID: syn70781006 |
| 16 | + # env vars related to testing the annotator.jar |
| 17 | + PROD_DOCKER: ghcr.io/sage-bionetworks/genie:main |
| 18 | + SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} |
| 19 | + TEST_PROJECT_SYNID: syn7208886 |
| 20 | +jobs: |
| 21 | + build-annotator: |
| 22 | + runs-on: ubuntu-latest |
| 23 | + |
| 24 | + steps: |
| 25 | + - name: Checkout workflow repo |
| 26 | + uses: actions/checkout@v4 |
| 27 | + |
| 28 | + - name: Set up Java |
| 29 | + uses: actions/setup-java@v4 |
| 30 | + with: |
| 31 | + java-version: ${{ env.JAVA_VERSION }} |
| 32 | + distribution: ${{ env.JAVA_DISTRIBUTION }} |
| 33 | + |
| 34 | + - name: Install Maven |
| 35 | + run: | |
| 36 | + wget https://archive.apache.org/dist/maven/maven-3/${MAVEN_VERSION}/binaries/apache-maven-${MAVEN_VERSION}-bin.zip |
| 37 | + unzip apache-maven-${MAVEN_VERSION}-bin.zip |
| 38 | + echo "$PWD/apache-maven-${MAVEN_VERSION}/bin" >> $GITHUB_PATH |
| 39 | +
|
| 40 | + - name: Install Python & Synapse client |
| 41 | + run: | |
| 42 | + python3 -m pip install --upgrade pip |
| 43 | + pip install synapseclient chardet |
| 44 | +
|
| 45 | + - name: Clone Genome Nexus Annotation Pipeline and check out commit hash |
| 46 | + run: | |
| 47 | + git clone https://github.com/genome-nexus/genome-nexus-annotation-pipeline.git |
| 48 | + cd genome-nexus-annotation-pipeline |
| 49 | + git checkout ${{ env.COMMIT_HASH }} |
| 50 | +
|
| 51 | + - name: Configure application.properties and log4j.properties to be GENIE-specific |
| 52 | + run: | |
| 53 | + cd genome-nexus-annotation-pipeline |
| 54 | + CONFIG_PATH="annotationPipeline/src/main/resources" |
| 55 | + mkdir -p "$CONFIG_PATH" |
| 56 | +
|
| 57 | + # Copy example configs first |
| 58 | + cp "${CONFIG_PATH}/application.properties.EXAMPLE" "${CONFIG_PATH}/application.properties" |
| 59 | + cp "${CONFIG_PATH}/log4j.properties.EXAMPLE" "${CONFIG_PATH}/log4j.properties" |
| 60 | +
|
| 61 | + # Modify application.properties lines in place |
| 62 | + sed -i \ |
| 63 | + -e 's|^spring.batch.job.enabled=.*|spring.batch.job.enabled=false|' \ |
| 64 | + -e 's|^spring.jmx.enabled=.*|spring.jmx.enabled=false|' \ |
| 65 | + -e 's|^chunk=.*|chunk=100|' \ |
| 66 | + -e 's|^genomenexus.enrichment_fields=.*|genomenexus.enrichment_fields=annotation_summary,sift,polyphen,my_variant_info|' \ |
| 67 | + -e 's|^genomenexus.isoform_query_parameter=.*|genomenexus.isoform_query_parameter=isoformOverrideSource|' \ |
| 68 | + -e 's|^genomenexus.base=.*|genomenexus.base=https://genie.genomenexus.org/|' \ |
| 69 | + "${CONFIG_PATH}/application.properties" |
| 70 | +
|
| 71 | + # Modify log4j.properties line |
| 72 | + sed -i \ |
| 73 | + -e 's|^log4j.appender.a.File.*|log4j.appender.a.File=/tmp/genomenexus-logfile.log|' \ |
| 74 | + "${CONFIG_PATH}/log4j.properties" |
| 75 | +
|
| 76 | + echo "[INFO] Application and log configs updated from EXAMPLE files." |
| 77 | +
|
| 78 | + - name: Build annotator.jar (skips tests) |
| 79 | + run: | |
| 80 | + cd genome-nexus-annotation-pipeline |
| 81 | + mvn clean install -DskipTests |
| 82 | + find . -name annotator.jar |
| 83 | +
|
| 84 | + - name: Upload annotator.jar, application.properties and log4j.properties to Synapse |
| 85 | + run: | |
| 86 | + cd genome-nexus-annotation-pipeline |
| 87 | + # Locate the built JAR dynamically |
| 88 | + FILE_PATH=$(ls -t annotationPipeline/target/annotationPipeline-*.jar | head -n 1) |
| 89 | +
|
| 90 | + if [ ! -f "$FILE_PATH" ]; then |
| 91 | + echo "Could not find annotationPipeline JAR under annotationPipeline/target/" |
| 92 | + echo "Available .jar files:" |
| 93 | + find annotationPipeline/target -type f -name "*.jar" || true |
| 94 | + exit 1 |
| 95 | + fi |
| 96 | +
|
| 97 | + echo "Found JAR: $FILE_PATH" |
| 98 | +
|
| 99 | + # Rename to annotator.jar |
| 100 | + TARGET_PATH="annotationPipeline/target/annotator.jar" |
| 101 | + cp "$FILE_PATH" "$TARGET_PATH" |
| 102 | +
|
| 103 | + echo "Renamed to: $TARGET_PATH" |
| 104 | + ls -lh "$TARGET_PATH" |
| 105 | +
|
| 106 | + echo "Uploading to Synapse entity ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }}..." |
| 107 | +
|
| 108 | + synapse login |
| 109 | +
|
| 110 | + # Upload annotator.jar file! |
| 111 | + synapse store "$TARGET_PATH" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }} |
| 112 | + |
| 113 | + # Upload application and log4j files |
| 114 | + CONFIG_PATH="annotationPipeline/src/main/resources" |
| 115 | + synapse store "${CONFIG_PATH}/application.properties" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }} |
| 116 | + synapse store "${CONFIG_PATH}/log4j.properties" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }} |
| 117 | + |
| 118 | + check-annotator-build: |
| 119 | + needs: build-annotator |
| 120 | + runs-on: ubuntu-latest |
| 121 | + steps: |
| 122 | + - name: Checkout repository |
| 123 | + uses: actions/checkout@v4 |
| 124 | + |
| 125 | + - name: Pull Public Docker Image from GHCR |
| 126 | + run: | |
| 127 | + docker pull ${{ env.PROD_DOCKER }} |
| 128 | +
|
| 129 | + - name: Start Docker Container |
| 130 | + run: | |
| 131 | + docker run -d --name genie-container \ |
| 132 | + -e SYNAPSE_AUTH_TOKEN="${{ env.SYNAPSE_AUTH_TOKEN }}" \ |
| 133 | + ${{ env.PROD_DOCKER }} \ |
| 134 | + sh -c "while true; do sleep 1; done" |
| 135 | + |
| 136 | + - name: Run processing on mutation data in test pipeline |
| 137 | + run: | |
| 138 | + docker exec genie-container \ |
| 139 | + python3 /root/Genie/bin/input_to_database.py mutation \ |
| 140 | + --project_id ${{ env.TEST_PROJECT_SYNID }} \ |
| 141 | + --genie_annotation_pkg /root/annotation-tools \ |
| 142 | + --createNewMafDatabase |
| 143 | +
|
| 144 | + - name: Stop and Remove Docker Container |
| 145 | + run: docker stop genie-container && docker rm genie-container |
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