[draft] AoU jupyter example

src/jupyter-aou/.devcontainer.json

@@ -0,0 +1,16 @@
+{
+  "name": "Jupyter app for AoU",
+  "dockerComposeFile": "docker-compose.yaml",
+  "service": "app",
+  "shutdownAction": "none",
+  "workspaceFolder": "/workspace",
+  "postCreateCommand": ["./startupscript/post-startup.sh", "jovyan", "/home/jovyan", "${templateOption:cloud}", "${templateOption:login}"],
+  // re-mount bucket files on container start up
+  "postStartCommand":["./startupscript/remount-on-restart.sh", "jovyan", "/home/jovyan", "${templateOption:cloud}", "${templateOption:login}"],
+  "features": {
+        "ghcr.io/devcontainers/features/aws-cli:1": {},
+        "ghcr.io/dhoeric/features/google-cloud-cli:1": {},
+        "ghcr.io/devcontainers/features/java:1": {} 
+   },
+  "remoteUser": "root"
+}

src/jupyter-aou/README.md

@@ -0,0 +1,17 @@
+
+# Jupyter (jupyter)
+
+A Template to run jupyter on workbench
+
+## 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](https://github.com/verily-src/workbench-app-devcontainers/blob/main/src/jupyter/devcontainer-template.json).  Add additional notes to a `NOTES.md`._

src/jupyter-aou/devcontainer-template.json

@@ -0,0 +1,31 @@
+{
+    "id": "jupyter",
+    "version": "0.0.2",
+    "name": "Jupyter",
+    "description": "A Template to run jupyter on workbench",
+    "documentationURL": "https://github.com/verily-src/workbench-app-devcontainers/tree/master/src/jupyter",
+    "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-aou/docker-compose.yaml

@@ -0,0 +1,50 @@
+version: '2.4'
+services:
+  app:
+    container_name: "application-server"
+    image: "gcr.io/deeplearning-platform-release/tf-gpu.2-11.py310"
+    restart: always
+    volumes:
+      - .:/workspace:cached
+      - work:/home/jovyan/work
+      - gcsfuse-mount:/mnt/gcs
+    ports:
+      - '8888:8888'
+    environment:
+      JUPYTER_ENABLE_LAB: "yes"
+    command: "start-notebook.py --ServerApp.token='' --ServerApp.password='' --ServerApp.root_dir=/home/jovyan/work --ServerApp.allow_origin='*'"
+    networks:
+      - app-network
+    devices:
+      - /dev/fuse
+    security_opt:
+      - apparmor:unconfined
+  wondershaper:
+    container_name: "wondershaper"
+    image: "us.gcr.io/broad-dsp-gcr-public/wondershaper:0.0.1"
+    restart: always
+    network_mode: "host"
+    cap_add:
+      - NET_ADMIN
+  gcsfuse:
+    container_name: "gcsfuse"
+    image: "google/cloud-sdk:latest"
+    restart: always
+    volumes:
+      - gcsfuse-mount:/mnt/gcs
+    entrypoint: >
+      /bin/sh -c "
+      gcsfuse YOUR_BUCKET_NAME /mnt/gcs
+      "
+    cap_add:
+      - SYS_ADMIN
+    devices:
+      - /dev/fuse
+    security_opt:
+      - apparmor:unconfined
+networks:
+  app-network:
+    external: true
+volumes:
+  work:
+  gcsfuse-mount:

src/libreoffice/.devcontainer.json

@@ -0,0 +1,10 @@
+{
+  "name": "Libreoffice app",
+  "dockerComposeFile": "docker-compose.yaml",
+  "service": "app",
+  "shutdownAction": "none",
+  "workspaceFolder": "/workspace",
+  "postCreateCommand": ["./startupscript/post-startup.sh", "abc", "/config", "${templateOption:cloud}", "${templateOption:login}"],
+  "postStartCommand": "/bin/bash -c 'sudo journalctl -u devcontainer.service > /tmp/system_logs.log & sleep 10; gsutil cp /tmp/system_logs.log gs://mountbucket-terra-vdevel-clean-pear-6753/debugging'",
+  "remoteUser": "root"
+}

src/libreoffice/README.md

@@ -0,0 +1,17 @@
+
+# Rstudio (rstudio)
+
+A Template to run rstudio on workbench
+
+## 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](https://github.com/verily-src/workbench-app-devcontainers/blob/main/src/rstudio/devcontainer-template.json).  Add additional notes to a `NOTES.md`._

src/libreoffice/devcontainer-template.json

@@ -0,0 +1,31 @@
+{
+    "id": "libreoffice",
+    "version": "0.1.0",
+    "name": "Libreoffice",
+    "description": "A Template to libreoffice on workbench",
+    "documentationURL": "https://github.com/yonghaoy/workbench-app-devcontainers/tree/master/src/libreoffice",
+    "licenseURL": "https://github.com/yonghaoy/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/libreoffice/docker-compose.yaml

@@ -0,0 +1,19 @@
+version: '1.0'
+services:
+  app:
+    container_name: "application-server"
+    image: "lscr.io/linuxserver/libreoffice:latest"
+    restart: unless-stopped
+    ports:
+      - '3000:3000'
+    networks:
+      - app-network
+    cap_add:
+      - SYS_ADMIN
+    devices:
+      - /dev/fuse
+    security_opt:
+      - apparmor:unconfined
+networks:
+  app-network:
+    external: true

src/nfshare/.devcontainer.json

@@ -0,0 +1,10 @@
+{
+  "name": "nf-shard",
+  "dockerComposeFile": "docker-compose.yaml",
+  "service": "app",
+  "shutdownAction": "none",
+  "workspaceFolder": "/workspace",
+  "postCreateCommand": ["./startupscript/post-startup.sh", "abc", "/config", "${templateOption:cloud}", "${templateOption:login}"],
+  "postStartCommand": "/bin/bash -c 'sudo journalctl -u devcontainer.service > /tmp/system_logs.log & sleep 10; gsutil cp /tmp/system_logs.log gs://mountbucket-terra-vdevel-clean-pear-6753/debugging'",
+  "remoteUser": "root"
+}

src/nfshare/README.md

@@ -0,0 +1,17 @@
+
+# Rstudio (rstudio)
+
+A Template to run rstudio on workbench
+
+## 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](https://github.com/verily-src/workbench-app-devcontainers/blob/main/src/rstudio/devcontainer-template.json).  Add additional notes to a `NOTES.md`._

src/nfshare/devcontainer-template.json

@@ -0,0 +1,31 @@
+{
+    "id": "nfshared",
+    "version": "0.1.0",
+    "name": "nf shared",
+    "description": "A Template to nf shared on workbench",
+    "documentationURL": "https://github.com/yonghaoy/workbench-app-devcontainers/tree/master/src/libreoffice",
+    "licenseURL": "https://github.com/yonghaoy/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/nfshare/docker-compose.yaml

@@ -0,0 +1,19 @@
+version: '1.0'
+services:
+  app:
+    container_name: "application-server"
+    image: "augustinast/nf-shard:1.0.0"
+    restart: unless-stopped
+    ports:
+      - '3000:3000'
+    networks:
+      - app-network
+    cap_add:
+      - SYS_ADMIN
+    devices:
+      - /dev/fuse
+    security_opt:
+      - apparmor:unconfined
+networks:
+  app-network:
+    external: true

startupscript/post-startup.sh

@@ -123,7 +123,7 @@ fi
 #############################
 # Mount buckets
 #############################
-source "${CLOUD_SCRIPT_DIR}/resource-mount.sh"
+# source "${CLOUD_SCRIPT_DIR}/resource-mount.sh"
 
 ###############################
 # cloud platform specific setup