recipe kleborate

Kleborate: a tool for typing and screening pathogen genome assemblies

Homepage:

https://kleborate.readthedocs.io/

Developer docs:

https://github.com/klebgenomics/Kleborate

License:

GPL3 / GPL-3.0-or-later

Recipe:

/kleborate/meta.yaml

Links:

doi: 10.1038/s41467-021-24448-3, doi: 10.1099/mgen.0.000102, biotools: kleborate, usegalaxy-eu: kleborate

package kleborate

(downloads) docker_kleborate

versions:
3.1.3-0,  3.1.2-0,  3.1.0-0,  3.0.9-0,  3.0.8-0,  3.0.6-0,  3.0.5-0,  2.3.2-0,  2.3.1-0, 

3.1.3-0,  3.1.2-0,  3.1.0-0,  3.0.9-0,  3.0.8-0,  3.0.6-0,  3.0.5-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.0-0,  2.1.0-1,  2.1.0-0,  2.0.4-1,  2.0.4-0,  2.0.3-0,  2.0.1-1,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.0.0-1,  1.0.0-0,  0.3.0-0

depends biopython:

>=1.83

depends dna_features_viewer:

depends kaptive:

depends mash:

depends minimap2:

depends numpy:

>=1.22

depends python:

>=3.9

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 kleborate

and update with::

   mamba update kleborate

To create a new environment, run:

mamba create --name myenvname kleborate

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/kleborate:<tag>

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

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