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17 changes: 2 additions & 15 deletions .github/workflows/test-xetabase-workflow.yml
Original file line number Diff line number Diff line change
Expand Up @@ -70,24 +70,11 @@ jobs:
distribution: 'temurin'
java-version: '8'
cache: 'maven'
- name: Install Samtools
run: sudo apt-get install samtools python3-deeptools
- name: Start MongoDB v6.0
uses: supercharge/mongodb-github-action@1.8.0
with:
mongodb-version: 6.0
mongodb-replica-set: rs-test
- name: K8s Tunnel MongoDB
run: |
wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
chmod +x ./kubectl
echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf &
- name: DockerHub login
uses: docker/login-action@v3
with:
username: ${{ env.DOCKER_HUB_USER }}
password: ${{ env.DOCKER_HUB_PASSWORD }}
- name: Install sshpass
run: sudo apt-get install sshpass
- name: Add SSH Host to known_hosts
Expand All @@ -97,11 +84,11 @@ jobs:
env:
SSH_HOST: ${{ env.SSH_HOST }}
SSH_PORT: ${{ env.SSH_PORT }}
- name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
- name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise
run: |
cd opencga-enterprise
ln -s ../opencga opencga-home
./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }}
- name: Upload reports results to Github
uses: actions/upload-artifact@v4
with:
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