recipe mbcgmlst

cgMLST allele calling pipeline with Ridom-style output.

Homepage:

https://github.com/liviurotiul/mbcgmlst

Documentation:

https://github.com/liviurotiul/mbcgmlst#readme

Developer docs:

https://github.com/liviurotiul/mbcgmlst/issues

License:

GPL / GPL-2.0-only

Recipe:

/mbcgmlst/meta.yaml

cgMLST allele calling pipeline that maps allele FASTA sequences against assembled genomes and emits a Ridom-style CSV.

package mbcgmlst

(downloads) docker_mbcgmlst

versions:

0.1.0-0

depends minimap2:

depends python:

>=3.9

depends tk:

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 mbcgmlst

and update with::

   mamba update mbcgmlst

To create a new environment, run:

mamba create --name myenvname mbcgmlst

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/mbcgmlst:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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