recipe shigatyper

Typing tool for Shigella spp. from WGS Illumina sequencing

Homepage:

https://github.com/CFSAN-Biostatistics/shigatyper

License:

Public Domain / Public Domain

Recipe:

/shigatyper/meta.yaml

package shigatyper

versions:

2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-0,  2.0.1-1,  2.0.1-0,  1.0.7-0,  1.0.6-0,  1.0.5-3

depends bcftools:

>=1.9

depends minimap2:

>=2.16

depends pandas:

>=0.24.2

depends python:

>=3.7

depends samtools:

>=1.9

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 shigatyper

and update with::

   mamba update shigatyper

To create a new environment, run:

mamba create --name myenvname shigatyper

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/shigatyper:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

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