Mercurial > repos > jjohnson > gatk2
comparison tool_dependencies.xml @ 5:0ed800373b59 draft
Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 02 Nov 2012 13:47:22 -0500 |
| parents | 5b2009fcf2ad |
| children | e5eac3c0ce10 |
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| 4:5b2009fcf2ad | 5:0ed800373b59 |
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| 17 <source>GenomeAnalysisTK.jar</source> | 17 <source>GenomeAnalysisTK.jar</source> |
| 18 <destination>$INSTALL_DIR</destination> | 18 <destination>$INSTALL_DIR</destination> |
| 19 </action> | 19 </action> |
| 20 <action type="set_environment"> | 20 <action type="set_environment"> |
| 21 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> | 21 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> |
| 22 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable> | 22 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD"</environment_variable> |
| 23 </action> | 23 </action> |
| 24 </actions> | 24 </actions> |
| 25 </install> | 25 </install> |
| 26 <readme> | 26 <readme> |
| 27 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: | 27 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: |