Mercurial > repos > iuc > bbtools_bbmerge

changeset 3:82ced0e47b9d draft

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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 6d084528a6f1
children 5d8b93c0731f
files bbmerge.xml macros.xml
diffstat 2 files changed, 7 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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}'
--- a/macros.xml	Sat Feb 10 17:55:55 2024 +0000
+++ b/macros.xml	Fri Apr 12 20:19:26 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">39.06</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>