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.
To compile and run Solvent as back-end component you need the following:
- Java 8 or higher (we recommend Oracle Java)
- Maven 3
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.
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.
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.
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.
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: