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comparison tool_dependencies.xml @ 8:e5eac3c0ce10 draft

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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>