Mercurial > repos > devteam > picard

diff picard_macros.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 6f9c0884a3e7
children 3f254c5ced1d
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line diff
--- a/picard_macros.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_macros.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -1,6 +1,4 @@
 <macros>
-    <token name="@TMPDIR_OPTION@">
-     `if [ -n "\$TMPDIR" ] ; then echo 'TMP_DIR=\$TMPDIR' ; else if [ -n "\$TEMP" ] ; then echo 'TMP_DIR=\$TEMP' ; fi ; fi`</token>
     <xml name="VS">
         <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
           <option value="LENIENT" selected="True">Lenient</option>
@@ -36,7 +34,7 @@
     ]]></token>
 
     <token name="@java_options@"><![CDATA[
-    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
+    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
     export _JAVA_OPTIONS &&
     ]]></token>