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comparison tool_dependencies.xml @ 1:ccadfae70b02 draft

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Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
author crs4
date Wed, 05 Mar 2014 06:48:08 -0500
parents 58e1eb37fddc
children 208ce57f9221
comparison
equal deleted inserted replaced
0:58e1eb37fddc 1:ccadfae70b02
2 <tool_dependency> 2 <tool_dependency>
3 <package name="bwa" version="0.6.2"> 3 <package name="bwa" version="0.6.2">
4 <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="blat" version="35"> 6 <package name="blat" version="35">
7 <!-- <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type --> 7 <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="sequel" version="1.0.2"> 9 <package name="sequel" version="1.0.2">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action> 12 <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action>
18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> 18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
19 </action> 19 </action>
20 <action type="set_environment"> 20 <action type="set_environment">
21 <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable> 21 <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
22 </action> 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> 23 </actions>
27 </install> 24 </install>
28 <readme> 25 <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). 26 Configuration: Previously (until Release 0), the SEQUEL_SITE_OPTIONS variable in the installed env.sh file was used 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). This is not used anymore and may be removed.
30 </readme> 27 </readme>
31 </package> 28 </package>
32 </tool_dependency> 29 </tool_dependency>