recipe snp-pipeline

Script and functions for SNP matrix construction

Homepage:

https://github.com/CFSAN-Biostatistics/snp-pipeline

License:

BSD License

Recipe:

/snp-pipeline/meta.yaml

package snp-pipeline

versions:

2.2.1-0,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.2-0,  1.0.1-2,  1.0.1-0,  0.7.0-0,  0.5.0-0

depends biopython:

depends jobrunner:

depends packaging:

depends psutil:

depends python:

depends pyvcf:

>=0.6.7

depends setuptools:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install snp-pipeline

and update with::

   mamba update snp-pipeline

To create a new environment, run:

mamba create --name myenvname snp-pipeline

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/snp-pipeline:<tag>

(see `snp-pipeline/tags`_ for valid values for ``<tag>``)

Download stats

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/snp-pipeline/README.html)