recipe metaamrplus

MetaAMRplus: unified detection of antimicrobial and metal resistance genes with colocalisation analysis

Homepage:

https://github.com/migshaw03/MetaAMRplus

License:

MIT

Recipe:

/metaamrplus/meta.yaml

MetaAMRplus is a command-line platform for the simultaneous identification of antimicrobial resistance genes, metal and biocide resistance genes, and their genomic colocalisation in bacterial genomes and plasmids. The tool integrates AMRFinder and BacMet databases and is designed for reproducible large-scale genomic analyses.

package metaamrplus

versions:

1.4.1-0,  1.4-0

depends awk:

depends blast:

depends ncbi-amrfinderplus:

depends pandas:

depends python:

>=3.8

depends wget:

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 metaamrplus

and update with::

   mamba update metaamrplus

To create a new environment, run:

mamba create --name myenvname metaamrplus

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/metaamrplus:<tag>

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

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