recipe ncbi-stxtyper

StxTyper identifies and types Stx operons from assembled genomic sequence.

Homepage:

https://github.com/ncbi/stxtyper

License:

Public Domain

Recipe:

/ncbi-stxtyper/meta.yaml

This software and the included database use a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence

package ncbi-stxtyper

(downloads) docker_ncbi-stxtyper

versions:

1.0.27-0,  1.0.25-0,  1.0.24-0

depends blast:

>=2.9

depends libgcc:

>=12

depends libstdcxx:

>=12

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 ncbi-stxtyper

and update with::

   mamba update ncbi-stxtyper

To create a new environment, run:

mamba create --name myenvname ncbi-stxtyper

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/ncbi-stxtyper:<tag>

(see `ncbi-stxtyper/tags`_ for valid values for ``<tag>``)

Download stats

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/ncbi-stxtyper/README.html)