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Remove thread options from base_recalibrator.xml
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 12:08:47 -0600
parents 7533db8dfb5b
children
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The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
copied into the tool-data directory.  The file tool_data_table_conf.xml must
be edited to include references to these two new files.  

GATK can be installed via tool_dependencies.   
This will install GenomeAnalysisTKLite.jar from ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/ 
and create a symbolic link from GenomeAnalysisTK.jar to GenomeAnalysisTKLite.jar

If you have a full licensed copy of GenomeAnalysisTK.jar, change the GenomeAnalysisTK.jar symbolic link 
in the installation directory to point to your licensed copy.

Two environment variables: GATK2_SITE_OPTIONS and GATK2_THREAD_OPTIONS  are also set in the tool_dependencies env.sh file.
You can alter the value of those variables for your site.
$ cat tool_dependencies/gatk/2.2/*/gatk2/*/env.sh
GATK2_PATH=/Users/jj/gxt/gxt/tool_dependencies/gatk/2.2/jimmy/gatk2/288cdae6bd9c; export GATK2_PATH
GATK2_SITE_OPTIONS="--phone_home STANDARD"; export GATK2_SITE_OPTIONS
GATK2_THREAD_OPTIONS="--num_threads 4 --num_cpu_threads_per_data_thread 3"; export GATK2_THREAD_OPTIONS