recipe gambitcore

Tool for rapid taxonomic identification of microbial pathogens

Homepage:

https://github.com/gambit-suite/gambitcore

License:

GPL / LGPL-3.0-or-later

Recipe:

/gambitcore/meta.yaml

A tool for bacterial species identification and assembly quality assessment. It evaluates assemblies by comparing their k-mer profiles against species-specific core genome references, providing both taxonomic identification and assembly completeness metrics.

package gambitcore

(downloads) docker_gambitcore

versions:

0.0.2-0

depends gambit:

depends libgcc:

>=13

depends pandas:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 gambitcore

and update with::

   mamba update gambitcore

To create a new environment, run:

mamba create --name myenvname gambitcore

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/gambitcore:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gambitcore/README.html)