Mercurial > repos > jjohnson > gatk2
diff README @ 18:7533db8dfb5b draft
Update tool_dependencies to GATK v 2.3
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 20 Dec 2012 11:01:55 -0600 |
| parents | 74c05070a3f8 |
| children |
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--- a/README Thu Nov 15 10:18:55 2012 -0600 +++ b/README Thu Dec 20 11:01:55 2012 -0600 @@ -2,4 +2,18 @@ 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 + +