Mercurial > repos > jjohnson > gatk2
comparison tool_dependencies.xml @ 8:e5eac3c0ce10 draft
Update tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 06 Nov 2012 11:41:15 -0600 |
| parents | 0ed800373b59 |
| children | 24504f5cac5e |
comparison
equal
deleted
inserted
replaced
| 7:f253357915e0 | 8:e5eac3c0ce10 |
|---|---|
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="gatk" version="2.2"> | 3 <package name="gatk" version="2.2"> |
| 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-latest.tar.bz2</action> | 6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action> |
| 7 <!-- this expands into GenomeAnalysisTKLite-2.2-2-gd3f5a5e/ | 7 <!-- this expands into GenomeAnalysisTKLite-2.2-3-g63dddfb/ |
| 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-2.2-3-g63dddfb 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-2.2-2-3-g63dddfb/GenomeAnalysisTKLite.jar</source> |
| 13 <destination>$INSTALL_DIR</destination> | 13 <destination>$INSTALL_DIR</destination> |
| 14 </action> | 14 </action> |
| 15 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> | 15 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> |
| 16 <action type="move_file"> | 16 <action type="move_file"> |
| 17 <source>GenomeAnalysisTK.jar</source> | 17 <source>GenomeAnalysisTK.jar</source> |