diff 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.

--- a/tool_dependencies.xml	Tue Oct 15 11:15:28 2013 -0400
+++ b/tool_dependencies.xml	Wed Mar 05 06:48:08 2014 -0500
@@ -4,7 +4,7 @@
     <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="blat" version="35">
-<!--    <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 -->
+    <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="sequel" version="1.0.2">
     <install version="1.0">
@@ -20,13 +20,10 @@
         <action type="set_environment">
           <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
         </action>
-        <action type="set_environment">
-          <environment_variable action="set_to" name="SEQUEL_SITE_OPTIONS">"-t 8 -p 8 -u 1"</environment_variable>
-        </action>
       </actions>
     </install>
     <readme>
-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).
+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.
     </readme>
   </package>
 </tool_dependency>