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comparison affy2vcf.xml @ 8:192da25388ec draft

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author greg
date Thu, 11 Oct 2018 14:20:31 -0400
parents 4dc497887a5c
children e981015b6b46
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7:4dc497887a5c 8:192da25388ec
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement> 4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #set text_outputs_dir = 'text_outputs' 7 #set text_outputs_dir = 'text_outputs'
8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
8 mkdir $text_outputs_dir && 9 mkdir $text_outputs_dir &&
9 bcftools +affy2vcf.so 10 bcftools +$BCFTOOLS_PLUGINS/affy2vcf.so
10 #if str($reference_genome_source_cond.reference_genome_source) == "history": 11 #if str($reference_genome_source_cond.reference_genome_source) == "history":
11 --fasta_ref '$reference_genome_source_cond.history_item' 12 --fasta_ref '$reference_genome_source_cond.history_item'
12 #else: 13 #else:
13 --fasta_ref '$reference_genome_source_cond.locally_cached_item' 14 --fasta_ref '$reference_genome_source_cond.locally_cached_item'
14 #end if 15 #end if