recipe bio_hansel

Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.

Homepage:

https://github.com/phac-nml/biohansel

License:

GPL3 / GNU General Public License v3 or later (GPLv3+)

Recipe:

/bio_hansel/meta.yaml

'Subtype Salmonella enterica genomes using 33bp k-mer typing schemes. ' 'Includes schemes for Heidelberg and Enteritidis subtyping.'

package bio_hansel

versions:

2.6.1-0,  2.5.0-0,  2.4.0-0,  2.2.0-1,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.0-1,  2.0.0-0, 

2.6.1-0,  2.5.0-0,  2.4.0-0,  2.2.0-1,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.0-1,  2.0.0-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.3-0,  1.1.1-0,  1.1.0-0,  0.2.0-1,  0.1.0-0

depends attrs:

depends numpy:

>=1.12.1

depends pandas:

>=0.20.1

depends pyahocorasick:

>=1.1.6

depends python:

>=3

depends rich:

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 bio_hansel

and update with::

   mamba update bio_hansel

To create a new environment, run:

mamba create --name myenvname bio_hansel

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/bio_hansel:<tag>

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

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