GPS web application

GPS is an integrated system designed specifically to support the use of clinical genomics in personalized medicine. This application is designed to assist a study team, manage the processes involved in gathering sequencing data and help experts correlate results with the clinical literature for reporting to physicians. The system tracks patients, samples, genomic sequencing information, clinical decisions, and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of mutations' tumor frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians.

Building GPS

We use Maven 3 as a build tool, and this should download and generate any dependencies required. So if you need to build the application, all you need to do is:

git clone [email protected]:oicr-ibc/gps.git
cd gps
mvn

Note that the default memory configuration for Java may not be sufficient to build the application, depending on your Java system. Using settings like export MAVEN_OPTS="-Xmx1024m -XX:MaxPermSize=256m" in your ~/.bash_profile or equivalent should be sufficient to build the application.

Running a local GPS

Also using Maven, once you have built the code as above, it is easy to start running a local copy of the application, using a command like this:

mvn -pl gps-webapp grails:run-app

This will start the application, by default at http://localhost:8080/gps-webapp. You can configure the application by setting any local values you need, for example to change the authentication system, in a local file at ~/.grails/gps-config.groovy.

Deploying GPS

If you want to deploy GPS on a Debian-based server, and happen to have installed the Debian packaging tools, you can make a new Debian package using the following command from Maven:

mvn -P ci-build

This will assemble a new package, at gps-server/target/gps-server-x.x.x.dpkg, which can be moved to your server and installed directly, using a command like:

sudo dpkg -i gps-server-x.x.x.dpkg

This is the recommended approach to server deployment, as the Debian package specifies all the dependencies, and the installer process configures the database. You'll then find configuration files under /etc/gps and can't start and stop the application using, for example, /etc/init.d/gps start.