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comparison bowtie2_wrapper.xml @ 21:e798c0b3384c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
author iuc
date Tue, 10 Apr 2018 18:39:49 -0400
parents fcc6efc4ef6d
children b2f8e8b8b9a3
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20:fcc6efc4ef6d 21:e798c0b3384c
7 <requirement type="package" version="2.3.4">bowtie2</requirement> 7 <requirement type="package" version="2.3.4">bowtie2</requirement>
8 <requirement type="package" version="1.6">samtools</requirement> 8 <requirement type="package" version="1.6">samtools</requirement>
9 </requirements> 9 </requirements>
10 <version_command>bowtie2 --version</version_command> 10 <version_command>bowtie2 --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## Use pipefail if available to quit with first non-zero exit code
13 set -o | grep -q pipefail && set -o pipefail;
12 ## prepare bowtie2 index 14 ## prepare bowtie2 index
13 #set index_path = '' 15 #set index_path = ''
14 #if str($reference_genome.source) == "history": 16 #if str($reference_genome.source) == "history":
15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && 17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
16 ln -s -f '$reference_genome.own_file' genome.fa && 18 ln -s -f '$reference_genome.own_file' genome.fa &&