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diff prokka.xml @ 3:fffa1ae330ae draft

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Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).
author crs4
date Mon, 09 Dec 2013 04:58:14 -0500
parents 4bafaa074484
children 5c0030f52b83
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--- a/prokka.xml	Fri Oct 25 08:59:51 2013 -0400
+++ b/prokka.xml	Mon Dec 09 04:58:14 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="prokka" name="Prokka" version="1.1.0">
+<tool id="prokka" name="Prokka" version="1.2.0">
   <description>prokaryotic genome annotation</description>
   <requirements>
     <requirement type="package" version="2.2.28">blast+</requirement>
@@ -6,15 +6,15 @@
     <requirement type="package" version="1.2.36">aragorn</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
     <requirement type="binary">tbl2asn</requirement>
-    <requirement type="binary">parallel</requirement>
-    <requirement type="package" version="0.2">barrnap</requirement>
-    <requirement type="package" version="1.1rc4">infernal</requirement>
+    <requirement type="package" version="20131122">gnu_parallel</requirement>
+    <requirement type="package" version="0.3">barrnap</requirement>
+    <requirement type="package" version="1.1">infernal</requirement>
     <requirement type="package" version="1.7">prokka</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
   <command>
     prokka
-    \${PROKKA_SITE_OPTIONS:---cpus 8}
+    --cpus \${GALAXY_SLOTS:-8}
     --quiet ## to avoid non-error messages written to stderr
     --outdir outdir --prefix prokka ## used in outputs section
     #if $locustag