recipe serotypefinder

SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli.

Homepage:

https://bitbucket.org/genomicepidemiology/serotypefinder

License:

APACHE / Apache-2.0

Recipe:

/serotypefinder/meta.yaml

Links:

doi: 10.1128/JCM.00008-1

package serotypefinder

(downloads) docker_serotypefinder

versions:

2.0.2-1,  2.0.2-0,  2.0.1-0

depends biopython:

>=1.79

depends blast:

>=2.8.1

depends cgecore:

>=1.5.5

depends git:

depends kma:

depends python:

>=3.8

depends tabulate:

>=0.8.9

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 serotypefinder

and update with::

   mamba update serotypefinder

To create a new environment, run:

mamba create --name myenvname serotypefinder

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/serotypefinder:<tag>

(see `serotypefinder/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/serotypefinder/README.html)