recipe ncbi-amrfinderplus

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

Homepage:

https://github.com/ncbi/amr

Documentation:

https://github.com/ncbi/amr/wiki

License:

Public Domain

Recipe:

/ncbi-amrfinderplus/meta.yaml

Links:

doi: 10.1038/s41598-021-91456-0

This software and the accompanying database are designed to find acquired antimicrobial resistance genes in bacterial protein or nucleotide sequences as well as known point mutations for several taxa. With AMRFinderPlus we have added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

package ncbi-amrfinderplus

versions:

4.0.3-0,  3.12.8-0,  3.11.26-0,  3.11.20-0,  3.11.18-0,  3.11.17-0,  3.11.14-1,  3.11.14-0,  3.11.11-1, 

4.0.3-0,  3.12.8-0,  3.11.26-0,  3.11.20-0,  3.11.18-0,  3.11.17-0,  3.11.14-1,  3.11.14-0,  3.11.11-1,  3.11.11-0,  3.11.4-0,  3.11.2-0,  3.10.45-0,  3.10.42-0,  3.10.40-1,  3.10.40-0,  3.10.36-1,  3.10.36-0,  3.10.30-1,  3.10.30-0,  3.10.24-0,  3.10.23-1,  3.10.23-0,  3.10.21-0,  3.10.20-0,  3.10.18-0,  3.10.16-0,  3.10.14-0,  3.10.5-0,  3.10.1-1,  3.10.1-0,  3.9.8-0,  3.9.3-0,  3.8.28-0,  3.8.4-1,  3.8.4-0,  3.6.15-0,  3.6.10-0,  3.6.7-0,  3.6.4-0,  3.2.3-0,  3.2.1-0,  3.1.1b-0,  3.0.12-0,  3.0.11-0,  3.0.9-0,  3.0.8-0

depends blast:

>=2.9

depends curl:

depends hmmer:

>=3.2

depends libcurl:

>=8.10.1,<9.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

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 ncbi-amrfinderplus

and update with::

   mamba update ncbi-amrfinderplus

To create a new environment, run:

mamba create --name myenvname ncbi-amrfinderplus

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/ncbi-amrfinderplus:<tag>

(see `ncbi-amrfinderplus/tags`_ for valid values for ``<tag>``)

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