recipe spotyping3

SpoTyping3: fast and accurate in silico Mycobacterium spoligotyping from sequence reads, compatible with Python3

Homepage:

https://github.com/matnguyen/SpoTyping

License:

GPL / GPL-3

Recipe:

/spotyping3/meta.yaml

Links:

DOI: 10.1186/s13073-016-0270-7

package spotyping3

(downloads) docker_spotyping3

versions:

3.0-0

depends blast:

depends python:

>=3.5

depends r-gdata:

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 spotyping3

and update with::

   mamba update spotyping3

To create a new environment, run:

mamba create --name myenvname spotyping3

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/spotyping3:<tag>

(see `spotyping3/tags`_ for valid values for ``<tag>``)

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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/spotyping3/README.html)