recipe resfinder

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.

Homepage:

https://bitbucket.org/genomicepidemiology/resfinder

Documentation:

https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md

License:

APACHE / Apache-2.0

Recipe:

/resfinder/meta.yaml

Links:

doi: 10.1093/jac/dkaa345

package resfinder

versions:

4.6.0-0,  4.5.0-0,  4.4.3-0,  4.4.2-1,  4.4.2-0,  4.1.11-0

depends biopython:

>=1.79

depends blast:

>=2.8.1

depends cgecore:

1.5.6

depends cgelib:

>=0.7.3

depends git:

depends kma:

depends pandas:

>=1.4.2

depends python:

>=3.9

depends python-dateutil:

depends tabulate:

>=0.8.9

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 resfinder

and update with::

   mamba update resfinder

To create a new environment, run:

mamba create --name myenvname resfinder

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/resfinder:<tag>

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

Notes

ResFinder requires databases that can be downloaded with download-db.sh.

Download stats

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