Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 32:e8b3f4f646b1

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Thu, 01 Feb 2018 16:20:17 -0500
parents c272b12525a6
children b6bc9158666c
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31:c272b12525a6 32:e8b3f4f646b1
1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10"> 1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
2 <description>into a multi-sample VCF with consensus SNPs</description> 2 <description>into a multi-sample VCF with consensus SNPs</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6">samtools</requirement>
5 <requirement type="package" version="1.6">bcftools</requirement> 4 <requirement type="package" version="1.6">bcftools</requirement>
6 <requirement type="package" version="1.0.6">bzip2</requirement> 5 <requirement type="package" version="1.0.6">bzip2</requirement>
7 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 6 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
8 <requirement type="package">tabix</requirement> 7 <requirement type="package" version="0.2.5">tabix</requirement>
9 <requirement type="package" version="3.4">python3</requirement> 8 <requirement type="package" version="3.4">python3</requirement>
9 <requirement type="package" version="1.6">htslib</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
13 env && 13 env &&
14 ls -lah \$CONDA_DEFAULT_ENV && 14 ls -lah \$CONDA_DEFAULT_ENV &&