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diff macros.xml @ 1:6ade12d94f9a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
author iuc
date Tue, 25 Sep 2018 04:21:24 -0400
parents 00d1f08bdcdc
children 02afb5ea2fce
line wrap: on
line diff
--- a/macros.xml	Wed Sep 19 08:21:51 2018 -0400
+++ b/macros.xml	Tue Sep 25 04:21:24 2018 -0400
@@ -67,6 +67,13 @@
         ##compute the number of ADDITIONAL threads to be used by samtools (-@)
         addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
     ]]></token>
+
+    <token name="@ADDMEMORY@"><![CDATA[
+        ##compute the number of memory available to samtools sort (-m)
+        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
+        ((addmemory=addmemory*75/100)) &&
+    ]]></token>
     <xml name="flag_options">
         <option value="1">read is paired</option>
         <option value="2">read is mapped in a proper pair</option>