Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.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
5 <requirement type="package" version="1.6">samtools</requirement> 5 <requirement type="package" version="1.6">samtools</requirement>
6 <requirement type="package" version="1.0.6">bzip2</requirement> 6 <requirement type="package" version="1.0.6">bzip2</requirement>
7 <requirement type="package">picard</requirement> 7 <requirement type="package">picard</requirement>
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="3.6">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 && 14 # env &&
15 python $__tool_directory__/snp-cache.py snp_sitecalls 15 python $__tool_directory__/snp-cache.py snp_sitecalls
16 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" 16 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
17 -c " 17 -c "
18 cp $input ./reference.fasta && 18 cp $input ./reference.fasta &&
19 samtools faidx ./reference.fasta && 19 samtools faidx ./reference.fasta &&