about the previous version of GATK

Question

[hnmcy11]

I am using Genome Strip to call large deletions, which needs GenomeAnalysisTK.jar and Queue.jar.It seems that the newest version (3.2.2) do not work.But GATK does not provide previous versions.How can I get the earlier vesion(GenomeAnalysisTK.jar and Queue.jar version 3.1)? Can anyone help me with that? Thank you!

Answer 1

[Garan]

EDIT: I've included some instructions below for compiling GATK by tag from source, but as you've mentioned in your comment your major is Biology and this is probably getting into Stack Overflow territory. Check again that GATK 3.2 isn't working and maybe try the GATK forum first before trying to compile from source.

You could try the Github repository and build from source

• https://github.com/broadgsa/gatk-protected/releases
• https://github.com/broadgsa/gatk/releases
• http://gatkforums.broadinstitute.org/discussion/3135/how-to-build-gatk

Just to clarify the initial stages

git clone https://github.com/broadgsa/gatk.git

This will clone the git repo which includes all the tagged versions, cd into the gatk directory

git tag -l

Will list the available tags - in the case of GATK this will be the version numbers

git checkout tags/3.1

This will checkout version 3.1 which should include the code you need - I'd better note that queue is in the protected-gatk repo so in this case you would do:

git clone https://github.com/broadgsa/gatk-protected.git

OS installed on: CentOS / Scientific Linux (if you're using Ubuntu or other distro the major steps are the same but the package manager will be different)

In order to build GATK you'll need the Java JDK and Maven

JDK

http://stackoverflow.com/questions/20901442/how-to-install-jdk-in-centos

yum install java-1.7.0-openjdk-devel

java -version
java version "1.7.0_65"
OpenJDK Runtime Environment (rhel-2.5.1.2.el6_5-x86_64 u65-b17)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

Maven

• http://maven.apache.org/download.cgi
• http://www.unixmen.com/install-apache-ant-maven-tomcat-centos-6-5/
• http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html

mvn -version

Apache Maven 3.2.3 (33f8c3e1027c3ddde99d3cdebad2656a31e8fdf4; 2014-08-11T21:58:10+01:00)
Maven home: /opt/maven
Java version: 1.7.0_65, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.65.x86_64/jre
Default locale: en_GB, platform encoding: ISO-8859-1
OS name: "linux", version: "2.6.32-358.23.2.el6.x86_64", arch: "amd64", family: "unix"

Navigate to the top level of the GATK directory and make sure that you have checked out the correct tag (i.e. "3.1"):

git checkout tags/3.1
mvn clean install

The build will take about 10 minutes since there's a few tests to run. The jar files will be in directories such as:

gatk/target/GenomeAnalysisTK.jar
/gatk/public/gatk-package/target/gatk-package-3.1.jar

[hnmcy11]

Thanks a lot for your sincere help! In fact my major is biology and know little about Java,so can you help me how to build the jar package from source in detail? Thanks in advance.

[hnmcy11]

Thanks a lot!