Mercurial > repos > crs4 > prokka

comparison prokka.xml @ 3:fffa1ae330ae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
2:4bafaa074484 3:fffa1ae330ae
1 <tool id="prokka" name="Prokka" version="1.1.0"> 1 <tool id="prokka" name="Prokka" version="1.2.0">
2 <description>prokaryotic genome annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.28">blast+</requirement> 4 <requirement type="package" version="2.2.28">blast+</requirement>
5 <requirement type="package" version="3.1b1">hmmer</requirement> 5 <requirement type="package" version="3.1b1">hmmer</requirement>
6 <requirement type="package" version="1.2.36">aragorn</requirement> 6 <requirement type="package" version="1.2.36">aragorn</requirement>
7 <requirement type="package" version="2.60">prodigal</requirement> 7 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="binary">tbl2asn</requirement> 8 <requirement type="binary">tbl2asn</requirement>
9 <requirement type="binary">parallel</requirement> 9 <requirement type="package" version="20131122">gnu_parallel</requirement>
10 <requirement type="package" version="0.2">barrnap</requirement> 10 <requirement type="package" version="0.3">barrnap</requirement>
11 <requirement type="package" version="1.1rc4">infernal</requirement> 11 <requirement type="package" version="1.1">infernal</requirement>
12 <requirement type="package" version="1.7">prokka</requirement> 12 <requirement type="package" version="1.7">prokka</requirement>
13 </requirements> 13 </requirements>
14 <version_command>prokka --version</version_command> 14 <version_command>prokka --version</version_command>
15 <command> 15 <command>
16 prokka 16 prokka
17 \${PROKKA_SITE_OPTIONS:---cpus 8} 17 --cpus \${GALAXY_SLOTS:-8}
18 --quiet ## to avoid non-error messages written to stderr 18 --quiet ## to avoid non-error messages written to stderr
19 --outdir outdir --prefix prokka ## used in outputs section 19 --outdir outdir --prefix prokka ## used in outputs section
20 #if $locustag 20 #if $locustag
21 --locustag "$locustag" 21 --locustag "$locustag"
22 #end if 22 #end if