recipe stecfinder

Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies

Homepage:

https://github.com/LanLab/STECFinder

License:

GPL3

Recipe:

/stecfinder/meta.yaml

package stecfinder

(downloads) docker_stecfinder

versions:

1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.0-0

depends blast:

>=2.9.0

depends kma:

>=1.3.15

depends python:

>=3.7

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 stecfinder

and update with::

   mamba update stecfinder

To create a new environment, run:

mamba create --name myenvname stecfinder

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/stecfinder:<tag>

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