Genome-wide Association Studies Pipeline

README

What is GWASpi?

• A tool to perform Genome-Wide Association Studies
• Written in Java, with Apache Derby, JFreeChart and NetCDF 3 technology
• Executable locally in a GUI (Graphical User Interface) and via command line

Getting Started

1. Obtain GWASpi
   • Get the latest stable version from the GWASpi homepage Download section, or
   • Get the latest testing version from the source hosting platform Download section, or
   • Get the latest development version by building it yourself from source
2. Obtain data
   • From the Tutorial section on the GWASpi homepage
   • From any other online source providing GWAS input data
3. Follow a tutorial
   • For general GWASpi usage, see the Introduction and the Tutorial sections on the GWASpi homepage
   • For COMBI instructions, see the (notoriously detailed) COMBI tutorial (local) (online) (or its Markdown version (local))
   • or just try clicking around!

Building

Maven is used as the project management system. The project description file is pom.xml, which contains everything Maven needs to know about the project, in order to:

• Download dependencies
• Compile the sources
• Pack the class files together with all the dependencies into a single, executable jar file

Installing Maven

You need Maven version 2 or later. In case you already have it installed, skip this paragraph.

• Windows

  Download the latest stable version (not the source) here. Then extract to eg. your C:\Program Files, and make sure the bin sub-dir of the extracted folder is in your PATH environment variable.

• Unix, Linux, BSD, OS X

  Install the maven2 package in your systems way of doing so. On Ubuntu for example, you would do this:

    > sudo apt-get install maven2
  

Building the software

1. Make sure you have Maven 2 or later installed. You can check that with the following command:

   > mvn --version
   

2. compile, package & install to the local repository:

   > mvn install
   

   This may take quite some time if you are running Maven for the first time, as it has to download all the dependencies for the different build steps, plus our own dependencies.

   NOTE: If this fails because the MOAPI framework dependency can not be found, you first have to run 'mvn install' in the MOAPI framework project.

All the output of the build process is under the target/ sub-dir. This is also where you find the final jar files.

Running

The preferred way of running the software while developing is through an IDE, or through Maven:

> mvn exec:java

An example with Java arguments (initial and maximum amount of RAM) and with application arguments (run in memory mode):

> MAVEN_OPTS="-Xms1024m -Xmx3g" mvn exec:java -Dexec.args="--memory"

Create Distribution Package

If you want to give the software to a non-dev for trying it out/using it, follow these instructions.

> mvn clean package assembly:single -DskipTests -P createUniqueBuild,compileWithJava6

You should end up with a single file to distribute at: target/gwaspi-{version}-jar-with-dependencies.jar

You can then use the file to start GWASpi like this:

> java -jar gwaspi-*jar-with-dependencies*.jar

An example with Java arguments (initial and maximum amount of RAM) and with application arguments (run in memory mode):

> java -Xms1024m -Xmx3g -jar gwaspi-*jar-with-dependencies*.jar --memory

Release a SNAPSHOT (devs only)

To release a development version to the Sonatype snapshot repository:

	mvn clean deploy

Release (devs only)

These instructions explain how to release to the Maven central repository.

Prepare "target/" for the release process

mvn release:clean

Prepare the release

• asks for the version to use

• packages

• signs with GPG

• commits

• tags

• pushes to origin

    mvn release:prepare
  

Perform the release (main part)

• checks-out the release tag

• builds

• deploy into Sonatype staging repository

    mvn release:perform
  

Release the site

• generates the site, and pushes it to the github gh-pages branch, visible under http://hoijui.github.com/GWASpi/

    git checkout <release-tag>
    mvn site
    git checkout master
  

Promote it on Maven

Moves it from the Sonatype staging to the main Sonatype repo

1. using the Nexus staging plugin:

    mvn nexus:staging-close
    mvn nexus:staging-release
   

2. ... alternatively, using the web-interface:

   • firefox https://oss.sonatype.org
   • login
   • got to the "Staging Repositories" tab
   • select "org.jorts..."
   • "Close" it
   • select "org.jorts..." again
   • "Release" it