Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 45:f58616a4b2f3

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Tue, 07 May 2019 11:44:12 -0400
parents 02733e77f84f
children d273453b30bb
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44:e7cac7790476 45:f58616a4b2f3
2 <description>for a sample, or lookup cached consensus SNP calls</description> 2 <description>for a sample, or lookup cached consensus SNP calls</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.6">bzip2</requirement> 4 <requirement type="package" version="1.0.6">bzip2</requirement>
5 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 5 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
6 <requirement type="package" version="1.5.11">boto3</requirement> 6 <requirement type="package" version="1.5.11">boto3</requirement>
7 <!-- <requirement type="package" version="3.5">python</requirement> --> 7 <requirement type="package" version="3.6">python</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
11 env && 11 # env &&
12 #set $identifier = $call_pileup.name.split(' ')[0] 12 #set $identifier = $call_pileup.name.split(' ')[0]
13 python $__tool_directory__/snp-cache.py snp_consenus_calls 13 python $__tool_directory__/snp-cache.py snp_consenus_calls
14 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 14 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
15 -c " 15 -c "
16 mkdir ./$identifier/ 16 mkdir ./$identifier/