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comparison tool_dependencies.xml @ 0:58e1eb37fddc draft

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author crs4
date Tue, 15 Oct 2013 11:15:28 -0400
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children ccadfae70b02
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-1:000000000000 0:58e1eb37fddc
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="bwa" version="0.6.2">
4 <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="blat" version="35">
7 <!-- <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
8 </package>
9 <package name="sequel" version="1.0.2">
10 <install version="1.0">
11 <actions>
12 <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action>
13 <action type="move_directory_files">
14 <source_directory>.</source_directory>
15 <destination_directory>$INSTALL_DIR</destination_directory>
16 </action>
17 <action type="set_environment">
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
19 </action>
20 <action type="set_environment">
21 <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
22 </action>
23 <action type="set_environment">
24 <environment_variable action="set_to" name="SEQUEL_SITE_OPTIONS">"-t 8 -p 8 -u 1"</environment_variable>
25 </action>
26 </actions>
27 </install>
28 <readme>
29 Change the SEQUEL_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u).
30 </readme>
31 </package>
32 </tool_dependency>