Mercurial > repos > simon-gladman > velvetoptimiser

changeset 4:4a53b89fa703 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 36de8aa1927d0204107371ffad76bdfe921be44a"
author iuc
date Wed, 13 Jan 2021 15:31:18 +0000
parents 37d88f41c810
children 82398ba86ba7
files velvetoptimiser.xml
diffstat 1 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/velvetoptimiser.xml	Tue Oct 30 20:29:42 2018 -0400
+++ b/velvetoptimiser.xml	Wed Jan 13 15:31:18 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6">
+<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy1">
     <description>Automatically optimize Velvet assemblies</description>
     <requirements>
         <requirement type="package" version="1.2.10">velvet</requirement>
@@ -6,8 +6,11 @@
     </requirements>
     <version_command>VelvetOptimiser.pl --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export OMP_NUM_THREADS=2 &&
-        export OMP_THREAD_LIMIT=2 &&
+        ## In Galaxy we do not us mutlithreading for the velvet
+        ## subprocesses, but only run multiple velvet calls in
+        ## parallel. Otherwise CPUs are overutilized.
+        export OMP_NUM_THREADS=1 &&
+        ## export OMP_THREAD_LIMIT=1 &&
         VelvetOptimiser.pl
             -t "\${GALAXY_SLOTS:-1}"
             -s $start_kmer