Downloading the GATK
From GSA
Contents |
Getting a Pre-Built Version
Within the Broad Institute
We stage a pre-built binary that members of the Broad community can use in the following directory:
/humgen/gsa-hpprojects/GATK/bin/current
We also archive older versions, indexed by version number, in /humgen/gsa-hpprojects/GATK/bin.
Outside the Broad Institute
A pre-built version of the GATK with basic tools is available from our ftp server.
ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTK-latest.tar.bz2
This URL will always point to the latest release-quality build of the GATK.
You can also visit:
ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/
to download any previously-released version of the GATK, or to determine whether a newer version of the GATK than you already have is available.
Please note that older versions of the GATK are completely unsupported.
Building the GATK from source
- Make sure you have suitable versions of the JDK and Ant. See the prerequisites section.
- You'll need a recent version of Git, which you can find here.
- Download the source from our Git repository. Run the following command:
git clone git://github.com/broadgsa/gatk.git destination_directory
- Use ant to build the source. The GATK uses the Ivy dependency manager to fetch all other dependencies:
cd destination_directory ant
- To get the latest updates once you already have a clone of our repository, do this from within your clone's directory:
git pull
- You can browse our repository's commit history by visiting our github page
- If you ever experience problems compiling or running the GATK after updating via a "git pull", try cleaning your clone's build directories before recompiling:
ant clean ant
Checking out a specific version of the GATK source
When you clone our github repository, you get not only the latest version of the GATK source, but all past versions as well. Here's how to check out a specific version of the source:
- If you haven't already cloned our github repository using the instructions above, you should start by doing so:
git clone git://github.com/broadgsa/gatk.git destination_directory cd destination_directory
- You need to know EITHER the version number or the commit ID for the version you want to check out:
Using a version number to check out a specific version of the GATK source
If you already know the version number of the version whose source you want to check out (eg., from running one of the pre-built binaries), your task is easy. Our version numbers look like this: "1.1-7-g6ebd834". Simply pass the version number to the "git checkout" command within your clone's directory:
git checkout version_number
For example:
git checkout 1.1-7-g6ebd834
You can now examine the source, compile, etc.
To switch back to the latest version, type:
git checkout master
Using a commit ID to check out a specific version of the GATK source
If you don't have a version number, you can still browse our commit history to find the commit ID for the version you want to check out. There are several ways to do this:
- If you type "git log", you can browse through the commit history locally. Search is available by typing a forward slash followed by the text you want to search for, then pressing enter. Press "n" to go to the next match. Once you've found the commit you want, note its commit ID number, which will look something like this: "6230315ff2ae7e7a000d064d98b403d7ef6383ec"
- If you visit our github page, you can get the commit ID's by browsing the commit history in the github web interface.
Once you have the commit ID for the version you want, you can check it out using the following command from within your clone's directory:
git checkout commit_id
For example:
git checkout 6230315ff2ae7e7a000d064d98b403d7ef6383ec
You can now examine the source, compile, etc.
To switch back to the latest version, type:
git checkout master
Signing up for email notifications whenever there's a new GATK release
If you want to receive an email whenever a new release of the GATK becomes available, please subscribe to our Gsa-announce mailing list.
Supplemental Files
For convenience, we also provide a GATK resource bundle
