diff --git a/src/gatk-demo/.devcontainer.json b/src/gatk-demo/.devcontainer.json new file mode 100644 index 00000000..28560022 --- /dev/null +++ b/src/gatk-demo/.devcontainer.json @@ -0,0 +1,54 @@ +{ + "name": "JupyterLab with GATK installed", + "dockerComposeFile": "docker-compose.yaml", + "service": "app", + "shutdownAction": "none", + "workspaceFolder": "/workspace", + "postCreateCommand": [ + "./startupscript/post-startup.sh", + "jupyter", + "/home/jupyter", + "${templateOption:cloud}", + "${templateOption:login}" + ], + // re-mount bucket files on container start up + "postStartCommand": [ + "./startupscript/remount-on-restart.sh", + "jupyter", + "/home/jupyter", + "${templateOption:cloud}", + "${templateOption:login}" + ], + "remoteUser": "root", + "customizations": { + "workbench": { + "opens": { + "extensions": [ + // Source + ".ipynb", + ".R", + ".py", + // Documents + ".md", + ".html", + ".latex", + ".pdf", + // Images + ".bmp", + ".gif", + ".jpeg", + ".jpg", + ".png", + ".svg", + // Data + ".csv", + ".tsv", + ".json", + ".vl" + ], + "fileUrlSuffix": "/lab/tree/{path}", + "folderUrlSuffix": "/lab/tree/{path}" + } + } + } +} diff --git a/src/gatk-demo/devcontainer-template.json b/src/gatk-demo/devcontainer-template.json new file mode 100644 index 00000000..1f937845 --- /dev/null +++ b/src/gatk-demo/devcontainer-template.json @@ -0,0 +1,33 @@ +{ + "id": "custom-workbench-jupyter-template", + "description": "A template used to serve the Workbench JupyterLab container image", + "version": "0.0.1", + "name": "Workbench Prebuilt JupyterLab Template", + "documentationURL": "https://github.com/verily-src/workbench-app-devcontainers/tree/master/src/custom-workbench-jupyter-template", + "licenseURL": "https://github.com/verily-src/workbench-app-devcontainers/blob/master/LICENSE", + "options": { + "cloud": { + "type": "string", + "description": "VM cloud environment", + "proposals": ["gcp", "aws"], + "default": "gcp" + }, + "login": { + "type": "string", + "description": "Whether to log in to workbench CLI", + "proposals": ["true", "false"], + "default": "false" + }, + "containerImage": { + "type": "string", + "description": "The container image to use", + "default": "us-central1-docker.pkg.dev/wb-fulgent-broccoli-5942/gatk-demo-repo/test1:20250225" + }, + "containerPort": { + "type": "number", + "description": "The port to expose the container on", + "default": 8888 + } + }, + "platforms": ["Any"] +} diff --git a/src/gatk-demo/docker-compose.yaml b/src/gatk-demo/docker-compose.yaml new file mode 100644 index 00000000..3bbea2c5 --- /dev/null +++ b/src/gatk-demo/docker-compose.yaml @@ -0,0 +1,22 @@ +version: "2.4" +services: + app: + container_name: "application-server" + image: "us-central1-docker.pkg.dev/wb-fulgent-broccoli-5942/gatk-demo-repo/test1:20250225" + user: "jupyter" + restart: always + volumes: + - .:/workspace:cached + ports: + - "8888:8888" + networks: + - app-network + cap_add: + - SYS_ADMIN + devices: + - /dev/fuse + security_opt: + - apparmor:unconfined +networks: + app-network: + external: true