Mercurial > repos > iuc > shovill

changeset 5:8d1af5db538d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
author iuc
date Sun, 28 Jun 2020 04:16:16 -0400
parents d9f6a00b6db7
children 83ead2be47b2
files shovill.xml
diffstat 1 files changed, 8 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/shovill.xml	Sun Aug 25 05:14:31 2019 -0400
+++ b/shovill.xml	Sun Jun 28 04:16:16 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0">
+<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1">
     <description>Faster SPAdes assembly of Illumina reads</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.4</token>
@@ -19,6 +19,13 @@
             ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
             ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
         #end if
+
+	## Sets the memory used by Shovill according to the following conditions
+	## (1) If SHOVILL_RAM is already set, use this value
+	## (2) Otherwise, set based on GALAXY_MEMORY_MB
+	## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset
+	GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) &&
+	SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} &&
         
         shovill
             --outdir 'out'