Auto-update Genome Nexus Truststore file #151
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| name: Auto-update Genome Nexus Truststore file | |
| on: | |
| schedule: | |
| - cron: "0 3 * * 1-5" # Runs at 3 AM UTC on Monday through Friday | |
| workflow_dispatch: | |
| env: | |
| PROD_DOCKER: ghcr.io/sage-bionetworks/genie:main | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} | |
| TRUSTSTORE_PASSWORD: ${{ secrets.GENOME_NEXUS_TRUSTSTORE_PWD }} # truststore password provided by GN team | |
| TEST_PROJECT_SYNID: syn7208886 # synapse_id of the test synapse project | |
| TEST_SEQ_DATE: Jul-2022 # SEQ_DATE to use for test pipeline. Should match the one used in nf-genie. | |
| jobs: | |
| update_truststore: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y keychain openssl | |
| pip install synapseclient | |
| - name: Authenticate with Synapse using token | |
| run: | | |
| synapse login -p "$SYNAPSE_AUTH_TOKEN" | |
| - name: Clone annotation-tools repository, checkout truststore branch and get truststore file | |
| run: | | |
| git clone https://github.com/genome-nexus/annotation-tools.git | |
| cd annotation-tools | |
| synapse get syn22053204 | |
| - name: Update truststore file | |
| run: | | |
| cd annotation-tools | |
| git checkout automate-truststore | |
| sh update_truststore.sh AwsSsl.truststore "$TRUSTSTORE_PASSWORD" | |
| - name: Upload updated truststore to Synapse | |
| run: | | |
| cd annotation-tools | |
| synapse store AwsSsl.truststore --parentid syn22105656 | |
| check-truststore-update: | |
| needs: update_truststore | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Pull Public Docker Image from GHCR | |
| run: | | |
| docker pull ${{ env.PROD_DOCKER }} | |
| - name: Start Docker Container | |
| run: | | |
| docker run -d --name genie-container \ | |
| -e SYNAPSE_AUTH_TOKEN="${{ secrets.SYNAPSE_AUTH_TOKEN }}" \ | |
| ${{ env.PROD_DOCKER }} \ | |
| sh -c "while true; do sleep 1; done" | |
| - name: Run processing on mutation data in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/input_to_database.py mutation \ | |
| --project_id ${{ env.TEST_PROJECT_SYNID }} \ | |
| --genie_annotation_pkg /root/annotation-tools \ | |
| --createNewMafDatabase | |
| - name: Run consortium release in test pipeline | |
| run: | | |
| docker exec genie-container \ | |
| python3 /root/Genie/bin/database_to_staging.py ${{ env.TEST_SEQ_DATE }} ../cbioportal TEST --test | |
| - name: Stop and Remove Docker Container | |
| run: docker stop genie-container && docker rm genie-container |