Mercurial > repos > crs4 > prokka
comparison prokka.xml @ 3:fffa1ae330ae draft
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 |
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date | Mon, 09 Dec 2013 04:58:14 -0500 |
parents | 4bafaa074484 |
children | 5c0030f52b83 |
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2:4bafaa074484 | 3:fffa1ae330ae |
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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 |