recipe pacini_typing

YAML-based bacterial genotyping application

Homepage:

https://github.com/RIVM-bioinformatics/Pacini-typing

License:

AGPL-3.0

Recipe:

/pacini_typing/meta.yaml

package pacini_typing

(downloads) docker_pacini_typing

versions:

1.6.3-01.6.1-0

depends biopython:

depends blast:

depends kma:

depends networkx:

depends numpy:

depends pandas:

depends pysam:

depends python:

>=3.10,<=3.12

depends pyyaml:

depends scipy:

depends tqdm:

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 pacini_typing

and update with::

   mamba update pacini_typing

To create a new environment, run:

mamba create --name myenvname pacini_typing

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/pacini_typing:<tag>

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

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