recipe ngs-chew

Simple QC and sanity checking of germline NGS data

Homepage:

https://github.com/bihealth/ngs-chew

License:

MIT / MIT

Recipe:

/ngs-chew/meta.yaml

package ngs-chew

versions:

0.9.4-0,  0.9.2-0,  0.8.1-0,  0.8.0-0,  0.7.1-0,  0.7.0-0,  0.6.0-0

depends attrs:

depends bcftools:

depends cattrs:

depends click:

depends logzero:

depends numpy:

depends pandas:

depends plotly:

depends pyarrow:

depends pysam:

depends python:

>=3.8

depends samtools:

depends scipy:

depends tqdm:

depends vcfpy:

requirements:

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 ngs-chew

and update with::

   mamba update ngs-chew

To create a new environment, run:

mamba create --name myenvname ngs-chew

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/ngs-chew:<tag>

(see `ngs-chew/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/ngs-chew/README.html)