recipe pmga

Command-line version of PMGA (PubMLST Genome Annotator) for all Neisseria species and Haemophilus influenzae

Homepage:

https://github.com/CDCgov/BMGAP

License:

AGPL / AGPL-2.0

Recipe:

/pmga/meta.yaml

Links:

doi: 10.3389/fgene.2020.601870

package pmga

versions:

3.0.2-0,  3.0.1-0

depends biopython:

>1.77

depends blast:

depends executor:

depends mash:

1.1.*

depends pigz:

depends python:

>=3.7

depends requests:

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 pmga

and update with::

   mamba update pmga

To create a new environment, run:

mamba create --name myenvname pmga

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/pmga:<tag>

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

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Link to this page

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