Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 48:fc7a28de6aa0

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Wed, 08 May 2019 11:10:14 -0400
parents 1667e4c08344
children e90a783a4e8b
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47:1667e4c08344 48:fc7a28de6aa0
8 <requirement type="package" version="1.6">htslib</requirement> 8 <requirement type="package" version="1.6">htslib</requirement>
9 <requirement type="package" version="3.7.3">python</requirement> 9 <requirement type="package" version="3.7.3">python</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
13 # env &&
14 ls -lah \$CONDA_DEFAULT_ENV/bin && 13 ls -lah \$CONDA_DEFAULT_ENV/bin &&
15 ls -lah \$CONDA_DEFAULT_ENV/lib && 14 ls -lah \$CONDA_DEFAULT_ENV/lib &&
16 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 15 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
17 #for $vcf in $vcfs 16 #for $vcf in $vcfs
18 -n $vcf.element_identifier -f $vcf 17 -n $vcf.element_identifier -f $vcf