hglive

HiGlass-backed dynamic BED gallery browser

This tool allows "live" browsing of BED files, rendering a specific HiGlass configuration at each BED element's genomic position.

The end user provides a BED file, and (optionally) specifies a custom HiGlass endpoint and view configuration ID.

The hglive tool is made up of a React frontend that mediates user interaction ("client"), and an Expressjs backend that handles BED and JSON coordinate and configuration files ("server").

Requirements

This tool is running on an Ubuntu 16 host. It should work on any Linux or Unix-like host that can run nodejs.

This tool requires a running HiGlass server instance, such as http://explore.altius.org or http://higlass.io, etc. and a unique view configuration ID that is exported from that instance. The view configuration holds collections of tracks in the desired presentation, similar to how a session ID associates to a collection of tracks in a UCSC Genome Browser instance.

The current test server includes defaults for server and view configuration ID settings that are currently valid. The end user may choose to create and export a custom view configuration on a HiGlass server instance, adding those server and view ID settings when importing their BED file.

Deployment

Update hostname

Update hostname references:

$ grep -rl oldhost . | xargs sed -i 's/oldhost/newhost/g'

The oldhost and newhost variables would be different EC2 hostnames, e.g.:

$ grep -rl ec2-1-2-3-4.us-east-2.compute.amazonaws.com | xargs sed -i 's/ec2-1-2-3-4.us-east-2.compute.amazonaws.com/ec2-9-8-7-6.us-east-2.compute.amazonaws.com/g'

Nodejs

Installation

$ cd ${HOME}
$ wget https://nodejs.org/dist/v10.11.0/node-v10.11.0-linux-x64.tar.xz
$ tar xvf node-v10.11.0-linux-x64.tar.xz
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/node /usr/bin/node
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/npm /usr/bin/npm
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/npx /usr/bin/npx

PM2

PM2 is used to manage the front- and backend services and logging.

Installation

$ sudo npm install pm2 -g
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/pm2 /usr/bin/pm2
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/pm2-dev /usr/bin/pm2-dev
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/pm2-docker /usr/bin/pm2-docker
$ sudo ln -sf ${HOME}/node-v10.11.0-linux-x64/bin/pm2-runtime /usr/bin/pm2-runtime
$ sudo pm2 startup systemd
$ sudo chown ubuntu:ubuntu /home/ubuntu/.pm2/rpc.sock /home/ubuntu/.pm2/pub.sock

Server

The following commands initialize the Expressjs service.

$ cd ${HOME}/git/hglive
$ mkdir assets
$ npm install --save
$ sudo pm2 start hglive-server.json

Client

The following commands generate a build distribution of the React application and initializes a process manager to serve the production application from port 80.

$ cd ${HOME}/git/hglive/hglive-client
$ npm install --save
$ npm run build
...
$ sudo npm install -g serve
$ sudo ln -s /home/ubuntu/node-v10.11.0-linux-x64/bin/serve /usr/bin/serve
$ sudo pm2 start hglive-client-production.json

The hglive-client-development.json object can be loaded instead, to run a development environment that recompiles the application as code is changed.

Persist PM2 setup

The following saves the PM2 process list, to restart services on reboot:

$ sudo pm2 save