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Last pushed: 5 days ago
Short Description
NodeJS express API for handling biological sequences
Full Description

seqservice

NodeJS express API for handling biological sequences

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

upstream api {
    server localhost:10030;
}

server {
   ...

    location /seqservice/socket.io {
        proxy_pass http://seqservice;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection "upgrade";
    }

    location /seqservice {
        proxy_http_version 1.1;
        proxy_set_header   X-Real-IP        $remote_addr;
        proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
        proxy_set_header   X-NginX-Proxy    true;
        proxy_set_header   Host             $http_host;
        proxy_set_header   Upgrade          $http_upgrade;
        proxy_redirect     off;
        proxy_pass         http://seqservice;
    }
    ...

}

Application start

From the directory of the application

npm install
npm run cpcss
npm run webpack
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

  • Keep track of submissions
  • 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
  • Save other analysis in DB
  • Download results in different formats (CSV, etc.)
  • Allow syncing with CouchDB
  • More coherent system of keeping params in configuration
  • Plug a task queue or submit to a cluster
  • Download databases if needed
Docker Pull Command
Owner
toniher
Source Repository

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