recipe mlst-cge

Multi Locus Sequence Typing (MLST) determine the ST from an assembled genome or from a set of reads.

Homepage:

https://bitbucket.org/genomicepidemiology/mlst

License:

APACHE / APACHE-2.0

Recipe:

/mlst-cge/meta.yaml

package mlst-cge

versions:

2.0.9-0

depends biopython:

depends blast:

>=2.8.1

depends cgecore:

1.5.5.*

depends kma:

depends python:

>=3

depends tabulate:

0.7.7.*

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 mlst-cge

and update with::

   mamba update mlst-cge

To create a new environment, run:

mamba create --name myenvname mlst-cge

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/mlst-cge:<tag>

(see `mlst-cge/tags`_ for valid values for ``<tag>``)

Notes

MLST requires a database that can be downloaded with download-db.sh.

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/mlst-cge/README.html)