Mercurial > repos > jjohnson > cdhit

diff tool_dependencies.xml @ 2:cca0838c1597

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Add an environment variable for the -M and -T options for memory and thread allocation
author Jim Johnson <jj@umn.edu>
date Tue, 26 Feb 2013 12:11:36 -0600
parents 34a799d173f7
children 88f9e90d9d78
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line diff
--- a/tool_dependencies.xml	Fri Sep 07 13:52:03 2012 -0500
+++ b/tool_dependencies.xml	Tue Feb 26 12:11:36 2013 -0600
@@ -7,6 +7,7 @@
                 <action type="shell_command">make openmp=yes</action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="CDHIT_SITE_OPTIONS" action="set_to">"-M 4000 -T 0"</environment_variable>
                 </action>
             </actions>
         </install>
@@ -19,6 +20,9 @@
 
 https://code.google.com/p/cdhit/source/browse/README
 
+Change the CDHIT_SITE_OPTIONS variable in the installed env.sh file to adjust 
+the maximum memory Mb (-M) or to limit the number of threads (-T)
+to match your site 
         </readme>
     </package>
 </tool_dependency>