https://github.com/alexpreynolds/hglive
HiGlass-backed dynamic BED gallery browser
https://github.com/alexpreynolds/hglive
bed bioinformatics expressjs higlass javascript react visualization
Last synced: 2 months ago
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HiGlass-backed dynamic BED gallery browser
- Host: GitHub
- URL: https://github.com/alexpreynolds/hglive
- Owner: alexpreynolds
- Created: 2018-10-19T17:07:49.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-11-01T15:30:20.000Z (over 7 years ago)
- Last Synced: 2025-09-09T03:51:35.191Z (9 months ago)
- Topics: bed, bioinformatics, expressjs, higlass, javascript, react, visualization
- Language: JavaScript
- Homepage: http://ec2-18-217-14-21.us-east-2.compute.amazonaws.com
- Size: 888 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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
```