recipe gambit

Tool for rapid taxonomic identification of microbial pathogens

Homepage:

https://github.com/jlumpe/gambit

Documentation:

https://gambit-genomics.readthedocs.io/en/latest

License:

AGPL / AGPL-3.0-or-later

Recipe:

/gambit/meta.yaml

Links:

doi: 10.1371/journal.pone.0277575, biotools: gambit_bacterial

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:

1.1.0-2,  1.1.0-1,  1.1.0-0,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.5.1-0,  0.5.0-0

depends _openmp_mutex:

>=4.5

depends attrs:

>=20

depends biopython:

>=1.79

depends cattrs:

>=23.2

depends click:

>=7.0

depends h5py:

>=3.0

depends libgcc:

>=13

depends numpy:

>=1.13,<2

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends scipy:

>=1.7

depends sqlalchemy:

>=1.4

depends typing-extensions:

>=4

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 gambit

and update with::

   mamba update gambit

To create a new environment, run:

mamba create --name myenvname gambit

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/gambit:<tag>

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

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