hgsoda

HiGlass soda plot gallery tool

Setup

Installation and testing is being done on an Ubuntu 16 host.

Some libraries are required for Puppeteer functionality:

$ sudo apt-get install libxss1 libnss3-dev -y

The hgsoda tool is made up of a React frontend that mediates user interaction, and an Express backend that handles turning BED files into browser snapshots.

Both the frontend and backend need to run on separate ports. Here's an example of how to start the development servers for each:

Backend

$ cd git/hgsoda
$ mkdir -p assets
$ npm install
$ export AWS_HOST="http://hgsoda.altius.org"
$ PORT=3000 HOST=${AWS_HOST} npm run dev

Frontend

$ cd git/hgsoda/client
$ npm install
$ export AWS_HOST="http://hgsoda.altius.org"
$ sudo PORT=80 HOST=${AWS_HOST} npm run start

PM2 deployment (production)

Installation

$ sudo npm install pm2 -g
$ sudo pm2 startup systemd
$ sudo npm i -g serve
$ sudo ln -s /home/ubuntu/node-v10.12.0-linux-x64/bin/serve /usr/bin/serve

Backend

We disable watch as the contents of this folder can change during snapshot processing. If watch is enabled, the node process will restart and potentially interrupt the creation of a gallery, which is bad.

$ cd git/hgsoda
$ cat > hgsoda-server.json
{
    apps : [
        {
            name: "hgsoda-server",
            script: "npm run build",
            interpreter: "node",
            watch: false,
	    cwd: "/home/ubuntu/git/hgsoda",
            env: {
                "DEBUG": "hgsoda:*",
                "PORT": 3000,
                "NODE_ENV": "production",
                "HOST": "hgsoda.altius.org"
            }
        }
    ]
}
$ sudo pm2 start hgsoda-server.json

Frontend

For the frontend, we serve a static build of the React application. We should be able to safely enable watch here, as we do not expect the contents of this folder to change. However, if we do change this folder's contents, this can affect the backend process and so we disable this parameter.

$ cd git/hgsoda/client
$ npm run build
$ cat > hgsoda-client.json
{
    apps : [
	{
	    name: "hgsoda-client",
	    script: "npx",
	    interpreter: "none",
	    watch: false,
	    cwd: "/home/ubuntu/git/hgsoda/client",
	    args: "serve -l 80 -s build"
	}
    ]
}
$ sudo pm2 start hgsoda-client.json

Other

Once pm2 is set up, use:

$ sudo pm2 save

to persist the process configuration between reboots of the host server.