Mercurial > repos > jjohnson > gatk2
comparison tool_dependencies.xml @ 2:a65944bad5c1 draft
tool_dependencies.xml - fix move_file and add symlink
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 01 Nov 2012 14:00:40 -0500 |
| parents | 9b8e2a158073 |
| children | 0edf813146d8 |
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| 1:9b8e2a158073 | 2:a65944bad5c1 |
|---|---|
| 8 which common_util.py tar_extraction_directory() does not find | 8 which common_util.py tar_extraction_directory() does not find |
| 9 so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path | 9 so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path |
| 10 --> | 10 --> |
| 11 <action type="move_file"> | 11 <action type="move_file"> |
| 12 <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source> | 12 <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source> |
| 13 <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination> | 13 <destination>$INSTALL_DIR</destination> |
| 14 </action> | 14 </action> |
| 15 <action type="shell_command">ln -s $INSTALL_DIR/GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> | |
| 15 <action type="set_environment"> | 16 <action type="set_environment"> |
| 16 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> | 17 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> |
| 17 </action> | 18 </action> |
| 18 <action type="set_environment"> | 19 <action type="set_environment"> |
| 19 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable> | 20 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable> |