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diff tool_dependencies.xml @ 2:b8c6a38530eb draft default tip

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Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA _SITE_OPTIONS. Directly call edena, remove edena_ovl_wrapper.py and edena_ass_wrapper.py . Discard stderr instead of redirecting to stdout. Do not redirect stdout to logfile. Add readme.rst .
author crs4
date Fri, 31 Jan 2014 12:08:21 -0500
parents 60609a9cef3b
children
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line diff
--- a/tool_dependencies.xml	Fri Oct 18 14:09:11 2013 -0400
+++ b/tool_dependencies.xml	Fri Jan 31 12:08:21 2014 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="edena" version="3.130110">
+  <package name="edena" version="3.131028">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://www.genomic.ch/edena/EdenaV3.130110.tar.gz</action>
+        <action type="download_by_url">http://www.genomic.ch/edena/EdenaV3.131028.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>bin</source_directory>
@@ -12,13 +12,10 @@
         <action type="set_environment">
           <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
         </action>
-        <action type="set_environment">
-          <environment_variable name="EDENA_SITE_OPTIONS" action="set_to">"--nThreads 2"</environment_variable>
-        </action>
       </actions>
     </install>
     <readme>
-Change the EDENA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use (--nThreads).
+Configuration: Previously (until Release 1), the EDENA_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--nThreads). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>