DO NOT MERGE: Test JupyterLab/GATK devcontainer based on workbench-ju…

src/jupyter-gatk/.devcontainer.json

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+{
+  "name": "Workbench JupyterLab with docker support devcontainer template",
+  "dockerComposeFile": "docker-compose.yaml",
+  "service": "app",
+  "shutdownAction": "none",
+  "workspaceFolder": "/workspace",
+  // Get the host's docker group ID and propagate it into the .env file, which
+  // allows it to be used within docker-compose.yaml.
+  "initializeCommand": "DOCKER_GID=`getent group docker | cut -d: -f3` && echo \"DOCKER_GID=${DOCKER_GID}\" > .env",
+  "postCreateCommand": "./startupscript/post-startup.sh jupyter /home/jupyter ${templateOption:cloud} ${templateOption:login} && ./startupscript/setup-docker.sh",
+  // re-mount bucket files on container start up
+  "postStartCommand": [
+    "./startupscript/remount-on-restart.sh",
+    "jupyter",
+    "/home/jupyter",
+    "${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}"
+      }
+    }
+  }
+}

src/jupyter-gatk/README.md

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+
+# Custom Workbench JupyterLab App Template (workbench-jupyter-docker)
+
+A template used to serve the Workbench custom JupyterLab app.
+
+## Options
+
+| Options Id | Description | Type | Default Value |
+|-----|-----|-----|-----|
+| cloud | VM cloud environment | string | gcp |
+| login | Whether to log in to workbench CLI | string | false |
+
+
+
+---
+
+_Note: This file was auto-generated from the [devcontainer-template.json](devcontainer-template.json).  Add additional notes to a `NOTES.md`._

src/jupyter-gatk/devcontainer-template.json

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+{
+  "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"
+    }
+  },
+  "platforms": ["Any"]
+}

src/jupyter-gatk/docker-compose.yaml

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+version: "2.4"
+services:
+  app:
+    container_name: "application-server"
+    image: "us-central1-docker.pkg.dev/wb-bright-turnip-4738/gatk-demo-repo/test1:20250226"
+    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