Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 40:02733e77f84f

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 14 Feb 2018 13:10:23 -0500
parents 69216317baa7
children f58616a4b2f3
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39:1fe3b14f7f1b 40:02733e77f84f
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="3.5">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" &&
11 env &&
10 #set $identifier = $call_pileup.name.split(' ')[0] 12 #set $identifier = $call_pileup.name.split(' ')[0]
11 python $__tool_directory__/snp-cache.py snp_consenus_calls 13 python $__tool_directory__/snp-cache.py snp_consenus_calls
12 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 14 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
13 -c " 15 -c "
14 mkdir ./$identifier/ 16 mkdir ./$identifier/