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comparison README @ 18:7533db8dfb5b draft

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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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17:f2b21dc45241 18:7533db8dfb5b
1 The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be 1 The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
2 copied into the tool-data directory. The file tool_data_table_conf.xml must 2 copied into the tool-data directory. The file tool_data_table_conf.xml must
3 be edited to include references to these two new files. 3 be edited to include references to these two new files.
4 4
5 GATK can be installed via tool_dependencies.
6 This will install GenomeAnalysisTKLite.jar from ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/
7 and create a symbolic link from GenomeAnalysisTK.jar to GenomeAnalysisTKLite.jar
5 8
9 If you have a full licensed copy of GenomeAnalysisTK.jar, change the GenomeAnalysisTK.jar symbolic link
10 in the installation directory to point to your licensed copy.
11
12 Two environment variables: GATK2_SITE_OPTIONS and GATK2_THREAD_OPTIONS are also set in the tool_dependencies env.sh file.
13 You can alter the value of those variables for your site.
14 $ cat tool_dependencies/gatk/2.2/*/gatk2/*/env.sh
15 GATK2_PATH=/Users/jj/gxt/gxt/tool_dependencies/gatk/2.2/jimmy/gatk2/288cdae6bd9c; export GATK2_PATH
16 GATK2_SITE_OPTIONS="--phone_home STANDARD"; export GATK2_SITE_OPTIONS
17 GATK2_THREAD_OPTIONS="--num_threads 4 --num_cpu_threads_per_data_thread 3"; export GATK2_THREAD_OPTIONS
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