Backend component of Concentrate – graphical tool for genomic data visualization
Switch branches/tags
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
src
.gitignore
LICENSE.txt
README.md
pom.xml

README.md

Solvent

Solvent is a server-side counterpart of Concentrate. Taken together they form a client-server system for genomic data visualization and filtering.

To getting started with Concentrate, please, see Getting Started guide.

Requirements

To compile and run Solvent as back-end component you need the following:

To build stand-alone Concentrate distribution additional components for front-end assembly should be installed:

Note that on some Linux distributions you should add node to path, e.g. by:

ln -s /usr/bin/nodejs /usr/bin/node

to prevent /usr/bin/env: node: No such file or directory error.

Build

To build stand-alone Concentrate use 'standalone' Maven profile:

mvn clean package -P standalone

To build Solvent without GUI run:

mvn clean package 

Both will produce WAR that can be directly executed by:

java -jar solvent-1.N.N-RELEASE.war

Or deployed on Tomcat server manually or using a command:

mvn tomcat7:deploy

Deploying parameters are specified in pom.xml and should be adopted to your environment.

Access

Solvent

To test back-end Solvent send GET HTTP request to:

http://localhost:8080/references

It is necessary to specify Accept header:

Accept: application/json

Full API description is available in project Wiki.

Concentrate

To use Concentrate for genomic data browsing start Concentrate with:

java -jar concentrate-1.N.N-RELEASE.war

And go to the following address in your web-browser:

localhost:8080

Concentrate UI should appear.

Work with references

This version of solvent grabs reference genome data from reference service. Reference service is a web application that provides access to genome sequences via RESTful API accompanied by web interface.

Publicly hosted reference service is available and can be accessed by the following URIs: