recipe haphpipe

HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.

Homepage

https://github.com/gwcbi/haphpipe

Documentation

https://gwcbi.github.io/haphpipe_docs/

License

GPL License

Recipe

/haphpipe/meta.yaml

package haphpipe

Versions

1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-1,  1.0.0-0

Depends

• biopython

• blast

• bowtie2

• bwa

• flash

• freebayes

• future

• gatk 3.8.*

• gsutil

• mafft

• modeltest-ng

• mummer

• picard

• python >=3.7

• pyyaml

• raxml-ng

• samtools >=1.9

• seqtk

• sierrapy

• spades

• sra-tools

• trimmomatic

Required By

Installation

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

conda install haphpipe

and update with:

conda update haphpipe

or use the docker container:

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

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

Link to this page

Render an 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/haphpipe/README.html)