Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.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
8 <requirement type="package">varscan</requirement> 8 <requirement type="package">varscan</requirement>
9 <requirement type="package" version="1.5.11">boto3</requirement> 9 <requirement type="package" version="1.5.11">boto3</requirement>
10 <!-- <requirement type="package" version="3.5">python</requirement> --> 10 <!-- <requirement type="package" version="3.5">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" &&
14 env &&
13 python $__tool_directory__/snp-cache.py snp_sitecalls 15 python $__tool_directory__/snp-cache.py snp_sitecalls
14 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" 16 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
15 -c " 17 -c "
16 cp $input ./reference.fasta && 18 cp $input ./reference.fasta &&
17 samtools faidx ./reference.fasta && 19 samtools faidx ./reference.fasta &&