QgeneS (Query genes Similarity) is a tool that lets you search for semantic relationships between genes. The result is shown as an interactive network.
This script setups the db, it builds the source code, it runs the servers and it deploy QgeneS.
./setup.sh [OPTION]
-h Display a help message.
-c Force the check of the dependencies.
- 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)
$ git clone https://github.com/mattux/qgenes.git
The OpenJDK package inside the repositories of your distribution should be OK. Otherwise, here you can find Java SE.
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
- open
Download the Full Platform flavor of Glassfish 4 (https://javaee.github.io/glassfish/download) and extract the archive in a directory (e.g. /opt/
).
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.
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
Assuming the code has been cloned in the home directory:
$ cd ~/qgenes/qgenes/
$ mvn package
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/