Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.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 ebfa7fd256aa
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47:1667e4c08344 48:fc7a28de6aa0
6 <requirement type="package" version="1.9.134">boto3</requirement> 6 <requirement type="package" version="1.9.134">boto3</requirement>
7 <requirement type="package" version="3.7.3">python</requirement> 7 <requirement type="package" version="3.7.3">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 &&
12 #set $identifier = $call_pileup.name.split(' ')[0] 11 #set $identifier = $call_pileup.name.split(' ')[0]
13 python $__tool_directory__/snp-cache.py snp_consenus_calls 12 python $__tool_directory__/snp-cache.py snp_consenus_calls
14 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 13 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
15 -c " 14 -c "
16 mkdir ./$identifier/ 15 mkdir ./$identifier/