add interactive mode

Sage-Bionetworks · Jan 8, 2025 · 01ff754 · 01ff754
1 parent a501218
commit 01ff754
Showing 1 changed file with 6 additions and 6 deletions.
diff --git 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 }} \
@@ -161,25 +161,25 @@ 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 \
             --createNewMafDatabase
     
     - 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