Package Recipe 'gambit'

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:

1.1.0-3, 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:

on _openmp_mutex >=4.5
on attrs >=20
on biopython >=1.79
on cattrs >=23.2
on click >=7.0,<8.2.0
on h5py >=3.0
on libgcc >=14
on numpy >=1.13,<2
on python >=3.10,<3.11.0a0
on python_abi 3.10.* *_cp310
on scipy >=1.7
on sqlalchemy >=1.4
on typing-extensions >=4

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install gambit

to add into an existing workspace instead, run:

pixi add gambit

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install gambit

Alternatively, to install into a new environment, run:

conda create -n envname gambit

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/gambit:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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/gambit/README.html)