recipe abricate

Mass screening of contigs for antibiotic resistance genes

Homepage:

https://github.com/tseemann/abricate

License:

GPL-2.0-only

Recipe:

/abricate/meta.yaml

Links:

biotools: ABRicate, usegalaxy-eu: abricate

package abricate

versions:

1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.9.9-0,  0.9.8-0,  0.9.7-0,  0.9.3-0,  0.8.13-0, 

1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.9.9-0,  0.9.8-0,  0.9.7-0,  0.9.3-0,  0.8.13-0,  0.8.10-0,  0.8.7-0,  0.8-1,  0.8-0,  0.7-2,  0.7-1,  0.7-0,  0.5-2,  0.5-1,  0.5-0,  0.4-2,  0.4-1,  0.4-0,  0.3-0,  0.2-1,  0.2-0

depends any2fasta:

depends blast:

>=2.7

depends perl-bioperl:

>=1.7

depends perl-json:

depends perl-list-moreutils:

depends perl-lwp-protocol-https:

depends perl-lwp-simple:

depends perl-path-tiny:

depends unzip:

depends zlib:

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 abricate

and update with::

   mamba update abricate

To create a new environment, run:

mamba create --name myenvname abricate

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/abricate:<tag>

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

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