- recipe gambit
Tool for rapid taxonomic identification of microbial pathogens
- Homepage:
- Documentation:
- License:
AGPL-3.0-or-later
- Recipe:
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens. It uses an extremely efficient genomic distance metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI RefSeq) to identify unknown bacterial genomes within seconds.
- package gambit¶
- versions:
1.0.0-0,0.5.1-0,0.5.0-0- depends alembic:
>=1.0- depends attrs:
>=20- depends biopython:
>=1.69- depends cattrs:
>=1.0- depends click:
>=7.0- depends h5py:
>=3.0- depends libgcc-ng:
>=12- depends numpy:
>=1.13- depends numpy:
>=1.23.3,<2.0a0- depends python:
>=3.10,<3.11.0a0- depends python_abi:
3.10.* *_cp310- depends scipy:
>=1.7- depends setuptools:
- depends sqlalchemy:
>=1.1- 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 gambit and update with:: mamba update gambit
To create a new environment, run:
mamba create --name myenvname gambit
with
myenvnamebeing 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/gambit:<tag> (see `gambit/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/gambit/README.html)
