Setup GATK and software packages required to follow the GATK Best Practices on Ubuntu 12.04 LTS.

You need to register an account at GATK, download the .tar.bz2 file, put it online somewhere, and change lines 9 and 10 of setup.sh

Or if you trust me, you can use the file I downloaded and saved in Dropbox.

Clone and run this on Ubuntu 12.04 LTS (use your best judgement for other system):

cd $HOME
sudo apt-get install -y git-core
git clone https://github.com/azalea/gatk_setup.git
./gatk_setup/setup.sh    

Most of the setup will run automatically.

Exceptions:

1. You need to agree to a license when installing Java.
2. You need to type "Y"

Testing if setup is successful:

source ~/.bashrc

# GATK
GATK --help
# wait and see lots of help messages
# The following should also work
# java -jar $GATK_HOME/GenomeAnalysisTK.jar --help

# Picard
java -jar $PICARD_HOME/AddOrReplaceReadGroups.jar -h 

bwa
samtools
htscmd
R
# in R console, type
# library(gsalib)