Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.xml @ 62:d497922d6caa

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planemo upload
author jpayne
date Fri, 28 Jun 2024 00:26:24 -0400
parents 2af5e948dd5c
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61:2af5e948dd5c 62:d497922d6caa
1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10"> 1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
2 <description>of high-confidence SNPs, or lookup cached sitecall</description> 2 <description>of high-confidence SNPs, or lookup cached sitecall</description>
3 <requirements> 3 <requirements>
4 <!-- <container type="docker">quay.io/biocontainers/mulled-v2-e518cb713b80020daa244e2ce559c37edb42dcde:5cb90165033bd74a97d0a807f439cf4b1aaabb89-0</container> --> 4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
5 <requirement type="package" version="2.4.5">bowtie2</requirement> 5 <!-- <requirement type="package" version="2.4.5">bowtie2</requirement>
6 <requirement type="package" version="1.9">samtools</requirement> 6 <requirement type="package" version="1.9">samtools</requirement>
7 <requirement type="package" version="1.0.8">bzip2</requirement> 7 <requirement type="package" version="1.0.8">bzip2</requirement>
8 <requirement type="package" version="2.27.4">picard</requirement> 8 <requirement type="package" version="2.27.4">picard</requirement>
9 <requirement type="package" version="2.4.4">varscan</requirement> 9 <requirement type="package" version="2.4.4">varscan</requirement>
10 <!-- <requirement type="package" version="1.9.134">boto3</requirement> --> 10 <requirement type="package" version="1.9.134">boto3</requirement> -->
11 <!-- <requirement type="package" version="3.6.8">python</requirement> --> 11 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 14 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
15 python $__tool_directory__/snp-cache.py snp_sitecalls 15 python $__tool_directory__/snp-cache.py snp_sitecalls