Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.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
9 <requirement type="package" version="1.9.134">boto3</requirement> 9 <requirement type="package" version="1.9.134">boto3</requirement>
10 <requirement type="package" version="3.7.3">python</requirement> 10 <requirement type="package" version="3.7.3">python</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
14 # env &&
15 python $__tool_directory__/snp-cache.py snp_sitecalls 14 python $__tool_directory__/snp-cache.py snp_sitecalls
16 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" 15 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
17 -c " 16 -c "
18 cp $input ./reference.fasta && 17 cp $input ./reference.fasta &&
19 samtools faidx ./reference.fasta && 18 samtools faidx ./reference.fasta &&