SNVPhyl Tools

This project will download and compile a number of dependency tools for the SNVPhyl whole genome phylogeny pipeline.

Legal

Copyright 2012-2017 Government of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Install Options

1. Install with bioconda (recommended)

conda install snvphyl-tools

2. Install dependencies using install_deps.sh

Script will download and compile in the current working directory bcftools,htslib, Mummer and Vcftools. Note that samtools version 1.9 needs to be available on the PATH and will not be installed by install_deps.sh .

Step a: Install Dependencies

---

git clone https://github.com/phac-nml/snvphyl-tools.git
cd snvphyl-tools
./install_deps.sh
#wait patiently to completion and setup the following environment variables
#example below
export PATH=/home/test/snvphyl-tools/bcftools-1.9:/home/test/snvphyl-tools/MUMmer3.23:$PATH
export BCFTOOLS_PLUGINS=/home/test//snvphyl-tools/bcftools-1.9/plugins
export PERL5LIB=/home/test/snvphyl-tools/lib/perl5

#Install samtools 1.9
#if conda available, use command below, else build with source or apt/yum
#conda install samtools samtools==1.9

Step b: Run Tests

---

In order to run the tests, please run the command:

$ prove
t/extract_snvs_metaalign.t ...... ok   
t/find-positions-used.t ......... ok   
t/variant_calls.t ............... ok     
t/vcf2core.t .................... ok    
All tests successful.
Files=6, Tests=232, 41 wallclock secs ( 0.28 usr  0.02 sys + 30.71 cusr  7.60 csys = 38.61 CPU)
Result: PASS