recipe pmlst

Plasmid Multi-Locus Sequence Typing

Homepage:

https://bitbucket.org/genomicepidemiology/pmlst

License:

APACHE / APACHE-2.0

Recipe:

/pmlst/meta.yaml

package pmlst

versions:

2.0.3-0

depends biopython:

depends blast:

>=2.8.1

depends cgecore:

1.5.5.*

depends kma:

depends python:

>=3

depends tabulate:

0.7.7.*

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 pmlst

and update with::

   mamba update pmlst

To create a new environment, run:

mamba create --name myenvname pmlst

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/pmlst:<tag>

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

Notes

pMLST requires database that can be downloaded with download-db.sh.

Download stats

Link to this page

Render an 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/pmlst/README.html)