diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d1943099..b4ec2a73 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -148,11 +148,11 @@ jobs: docker run -d --name genie-container \ -e SYNAPSE_AUTH_TOKEN="${{ secrets.SYNAPSE_AUTH_TOKEN }}" \ ghcr.io/sage-bionetworks/genie:${{ github.ref_name }} \ - -c "while true; do sleep 1; done" + /bin/bash -c "while true; do sleep 1; done" - name: Run validation in test pipeline run: | - docker exec genie-container \ + docker exec -it genie-container /bin/bash \ python3 /root/Genie/bin/input_to_database.py \ mutation \ --project_id ${{ env.TEST_PROJECT_SYNID }} \ @@ -161,12 +161,12 @@ jobs: - name: Run processing on non-mutation data in test pipeline run: | - docker exec genie-container \ + docker exec -it genie-container /bin/bash \ python3 /root/Genie/bin/input_to_database.py main --project_id ${{ env.TEST_PROJECT_SYNID }} --deleteOld - name: Run processing on mutation data in test pipeline run: | - docker exec genie-container \ + docker exec -it genie-container /bin/bash \ python3 /root/Genie/bin/input_to_database.py mutation --project_id ${{ env.TEST_PROJECT_SYNID }} \ --deleteOld \ --genie_annotation_pkg /root/annotation-tools \ @@ -174,12 +174,12 @@ jobs: - name: Run consortium release in test pipeline run: | - docker exec genie-container \ + docker exec -it genie-container /bin/bash \ python3 /root/Genie/bin/database_to_staging.py Jan-2017 ../cbioportal TEST --test - name: Run public release in test pipeline run: | - docker exec genie-container \ + docker exec -it genie-container /bin/bash \ python3 /root/Genie/bin/consortium_to_public.py Jan-2017 ../cbioportal TEST --test - name: Stop and Remove Docker Container