diff --git a/http/src/main/resources/init-resources/gce-init.sh b/http/src/main/resources/init-resources/gce-init.sh index d784e8a444..124075a003 100644 --- a/http/src/main/resources/init-resources/gce-init.sh +++ b/http/src/main/resources/init-resources/gce-init.sh @@ -276,6 +276,14 @@ STEP_TIMINGS+=($(date +%s)) log 'Starting up the Jupyter...' + +# Start gcsfuse as a sidecar +mkdir -p /mnt/disks/bucket +docker run -d --name gcsfuse-container --privileged -u root -e PIP_USER=false --env BUCKET_NAME=genomics-public-data --device /dev/fuse:/dev/fuse --security-opt apparmor=unconfined -v /mnt/disks/bucket:/mnt/gcs-bucket:shared tarekmahmed/gcsfuse-container:latest +# Use docker compose here +# $(DOCKER_COMPOSE) -f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename gcsfuse-docker-compose-gce.yaml` config + + # Run docker-compose for each specified compose file. # Note the `docker-compose pull` is retried to avoid intermittent network errors, but # `docker-compose up` is not retried since if that fails, something is probably broken diff --git a/http/src/main/resources/init-resources/init-actions.sh b/http/src/main/resources/init-resources/init-actions.sh index 21bbcb9189..8f5d8237e5 100644 --- a/http/src/main/resources/init-resources/init-actions.sh +++ b/http/src/main/resources/init-resources/init-actions.sh @@ -304,6 +304,13 @@ END log 'Starting up the Jupydocker...' + # Start gcsfuse as a sidecar + mkdir -p /mnt/disks/bucket + docker run -d --name gcsfuse-container --privileged -u root -e PIP_USER=false --env BUCKET_NAME=genomics-public-data --device /dev/fuse:/dev/fuse --security-opt apparmor=unconfined -v /mnt/disks/bucket:/mnt/gcs-bucket:shared tarekmahmed/gcsfuse-container:latest + # Use docker compose here + # $(DOCKER_COMPOSE) -f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename gcsfuse-docker-compose-gce.yaml` config + + # Run docker-compose for each specified compose file. # Note the `docker-compose pull` is retried to avoid intermittent network errors, but # `docker-compose up` is not retried. diff --git a/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml b/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml index fd782503b2..a15355a7a2 100644 --- a/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml +++ b/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml @@ -19,6 +19,7 @@ services: volumes: # shared with welder - "/mnt/disks/work:${NOTEBOOKS_DIR}" + - /mnt/disks/bucket:/usr/local/genomics:shared restart: always environment: GOOGLE_PROJECT: "${GOOGLE_PROJECT}" diff --git a/http/src/main/resources/init-resources/jupyter-docker-compose.yaml b/http/src/main/resources/init-resources/jupyter-docker-compose.yaml index c933c1e575..161440f120 100644 --- a/http/src/main/resources/init-resources/jupyter-docker-compose.yaml +++ b/http/src/main/resources/init-resources/jupyter-docker-compose.yaml @@ -36,6 +36,7 @@ services: - /hadoop:/hadoop - /hadoop_gcs_connector_metadata_cache:/hadoop_gcs_connector_metadata_cache - /usr/local/share/google/dataproc:/usr/local/share/google/dataproc + - /mnt/disks/bucket:/usr/local/genomics:shared restart: always environment: GOOGLE_PROJECT: "${GOOGLE_PROJECT}"