Mercurial > repos > iuc > bbtools_bbmerge

diff bbmerge.xml @ 3:82ced0e47b9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
author: iuc
date: Fri, 12 Apr 2024 20:19:26 +0000
parents: fc029a9b4d07
children: 5d8b93c0731f
--- a/bbmerge.xml	Sat Feb 10 17:55:55 2024 +0000
+++ b/bbmerge.xml	Fri Apr 12 20:19:26 2024 +0000
@@ -39,7 +39,12 @@
     ln -s '${read2}' '${read2_file}' &&
 #end if
 
-bbmerge.sh
+if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
+    export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
+fi &&
+
+bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"
+
 #### Input parameters
 #if str($input_type_cond.input_type) == 'single':
     in='${read1_file}'