Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.xml @ 9:41bd2a5793ee

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 15:55:32 -0500
parents 360e1c2bf24d
children 25b858c2f21d
comparison
equal deleted inserted replaced
8:360e1c2bf24d 9:41bd2a5793ee
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="3.4">python</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 $__tool_directory__/snp-cache.py snp_sitecalls 13 python $__tool_directory__/snp-cache.py snp_sitecalls
14 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" 14 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
15 -c " 15 -c "
16 cp $input ./reference.fasta && 16 cp $input ./reference.fasta &&
17 samtools faidx ./reference.fasta && 17 samtools faidx ./reference.fasta &&
18 samtools view -bS -F 4 $sample | 18 samtools view -bS -F 4 $sample |