Mercurial > repos > jjohnson > gatk2
comparison tool_dependencies.xml @ 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 | 35c6289faeff |
| children | 09e6427d3e6a |
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| 17:f2b21dc45241 | 18:7533db8dfb5b |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="gatk" version="2.2"> | 3 <package name="gatk" version="2.3"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2</action> | 6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.3-4-gb8f1308.tar.bz2</action> |
| 7 <action type="move_file"> | 7 <action type="move_file"> |
| 8 <source>GenomeAnalysisTKLite.jar</source> | 8 <source>GenomeAnalysisTKLite.jar</source> |
| 9 <destination>$INSTALL_DIR</destination> | 9 <destination>$INSTALL_DIR</destination> |
| 10 </action> | 10 </action> |
| 11 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> | 11 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> |
| 13 <source>GenomeAnalysisTK.jar</source> | 13 <source>GenomeAnalysisTK.jar</source> |
| 14 <destination>$INSTALL_DIR</destination> | 14 <destination>$INSTALL_DIR</destination> |
| 15 </action> | 15 </action> |
| 16 <action type="set_environment"> | 16 <action type="set_environment"> |
| 17 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> | 17 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> |
| 18 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD"</environment_variable> | 18 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--phone_home STANDARD"</environment_variable> |
| 19 <environment_variable name="GATK2_THREAD_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3"</environment_variable> | |
| 19 </action> | 20 </action> |
| 20 </actions> | 21 </actions> |
| 21 </install> | 22 </install> |
| 22 <readme> | 23 <readme> |
| 23 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: | 24 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: |