Public | Automated Build

Last pushed: 25 days ago
Short Description
NodeJS express API for handling biological sequences
Full Description

seqservice

NodeJS express API for handling biological sequences analyses

INSTALLATION

Server configuration

  • Dependencies

    • NCBI-BLAST
    • Samtools (optional)
  • Assuming we define /seqservice as basepath, and we keep 10030 port in config.json

Apache

# Reverse proxy seqservice
RewriteEngine On
RewriteRule ^/seqservice/(.*)$ http://localhost:10030/seqservice/$1 [P]

ProxyPass        /seqservice/socket.io http://localhost:10030/seqservice/socket.io
ProxyPassReverse /seqservice/socket.io http://localhost:10030/seqservice/socket.io

NGINX

Check example nginx.conf file

Application start

From the directory of the application

npm install
npm run build
NODE_ENV=production node index.js

FUN!

Docker installation

From this repository:

sudo docker build -t seqservice .
sudo docker run -p 10030:10030 -d seqservice

Open your browser at http://localhost:10030/seqservice/

TODO

  • FIXING Websocket access behind proxies such as NGINX
  • Webpack: Consider putting manifest for hashed version
  • Webpack and npm run: enable proper PRODUCTION and DEVELOPMENT behaviour
  • Allow single-hit accompanying analyses (e.g. ProtLoc or GO)
  • Generate alignment from results at user's choice
  • Start PSIBLAST from user choice of sequences
  • Include more HMMER options
  • Download results in different formats (CSV, etc.)
  • Allow syncing/saving with a DB (e. g. CouchDB)
  • Plug a task queue. By using https://github.com/paulmillr/chokidar and maybe Nextflow
  • Download input databases if needed (through CLI or web interface)
  • Plug an embeddable Genome Browser (e. g. igv.js)
  • More coherent system of keeping params in configuration for more different analyses
  • Fix error when PouchDB executed for first time (empty store)
Docker Pull Command
Owner
toniher
Source Repository