Mercurial > repos > devteam > picard
diff picard_macros.xml @ 32:f9242e01365a draft
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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--- 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>