Mercurial > repos > crs4 > sequel
annotate tool_dependencies.xml @ 1:ccadfae70b02 draft
Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
author | crs4 |
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date | Wed, 05 Mar 2014 06:48:08 -0500 |
parents | 58e1eb37fddc |
children | 208ce57f9221 |
rev | line source |
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0 | 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"> | |
1
ccadfae70b02
Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
crs4
parents:
0
diff
changeset
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7 <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> |
0 | 8 </package> |
9 <package name="sequel" version="1.0.2"> | |
10 <install version="1.0"> | |
11 <actions> | |
12 <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action> | |
13 <action type="move_directory_files"> | |
14 <source_directory>.</source_directory> | |
15 <destination_directory>$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 </actions> | |
24 </install> | |
25 <readme> | |
1
ccadfae70b02
Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
crs4
parents:
0
diff
changeset
|
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. |
0 | 27 </readme> |
28 </package> | |
29 </tool_dependency> |