recipe phenix

Public Health England SNP calling pipeline

Homepage

https://github.com/phe-bioinformatics/PHEnix

License

GPL3

Recipe

/phenix/meta.yaml

Links

biotools: phenix

package phenix

(downloads) docker_phenix

Versions

1.4.1a-0

Depends argparse

Depends bcftools

Depends bintrees

Depends biopython

Depends bowtie2

Depends bwa

Depends gatk

Depends matplotlib

Depends matplotlib-venn

Depends numpy

Depends picard

Depends psycopg2

Depends pysam

Depends python

>=2.7,<2.8.0a0

Depends pyvcf

Depends pyyaml

Depends samtools

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install phenix

and update with:

conda update phenix

or use the docker container:

docker pull quay.io/biocontainers/phenix:<tag>

(see phenix/tags for valid values for <tag>)

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/phenix/README.html)