QgeneS

QgeneS (Query genes Similarity) is a tool that lets you search for semantic relationships between genes. The result is shown as an interactive network.

Setup script

This script setups the db, it builds the source code, it runs the servers and it deploy QgeneS.

Usage:

./setup.sh [OPTION]

-h    Display a help message.
-c    Force the check of the dependencies.

Getting ready (on a Linux machine)

Requires:

Java JDK (Oracle or OpenJDK), min. 1.7
Maven (min 3.0)
Glassfish (min. 4)
Neo4j (from 2.2 to 3.2 - with above versions QgeneS may not work properly)

1) Download the source code

$ git clone https://github.com/mattux/qgenes.git

2) Install Java JDK

The OpenJDK package inside the repositories of your distribution should be OK. Otherwise, here you can find Java SE.

3) Install Neo4j

Get it from http://neo4j.com/download/.

Extract in a directory of your choice (e.g. /opt/).

Note: QgeneS assumes that:

the database server URL is localhost:7474 (is the default configuration)
the authentication is disabled; to disable it:
- open /opt/neo4j-community-{YOUR_VERSION}/conf/neo4j.conf
- the line dbms.security.auth_enabled must be =false

3) Install Glassfish 4

Download the Full Platform flavor of Glassfish 4 (https://javaee.github.io/glassfish/download) and extract the archive in a directory (e.g. /opt/).

4) Install Maven

If it is not present in your distribution's repo, take it from here: http://maven.apache.org/download.html

And here how to install manually.

Build and run, manually (on a Linux machine)

Populate and run the database

Download the datasets from here: https://gitlab.com/mattux/qgenes_datasets/tree/master.

Populate the db (check your neo4j version):

# /opt/neo4j-community-{YOUR_VERSION}/bin/neo4j-import --into {DESTINATION} --nodes "{PATH_OF_GENES_DATASET}" --relationships "{PATH_OF_SIMILARITIES_DATASET}" --delimiter "|" --array-delimiter ";"

Launch Neo4j:

# /opt/neo4j-community-{YOUR_VERSION}/bin/neo4j start

Build the source code

Assuming the code has been cloned in the home directory:

$ cd ~/qgenes/qgenes/
$ mvn package

Deploy and run the application server

Assuming Glassfish is located in /opt:

# /opt/glassfish4/bin/asadmin start-domain
# /opt/glassfish4/bin/asadmin deploy --name qgenes /home/{USER}/qgenes/qgenes/target/qgenes.war

In the browser, go to:

http://localhost:8080/qgenes/

mattux / qgenes