recipe bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Homepage:

https://github.com/jenniferlu717/Bracken

Documentation:

https://github.com/jenniferlu717/Bracken/blob/v3.0/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/bracken/meta.yaml

Links:

biotools: Bracken, usegalaxy-eu: est_abundance, doi: 10.7717/peerj-cs.104

package bracken

(downloads) docker_bracken

versions:
3.0-0,  2.9-1,  2.9-0,  2.8-1,  2.8-0,  2.7-0,  2.6.2-0,  2.6.1-3,  2.6.1-2, 

3.0-0,  2.9-1,  2.9-0,  2.8-1,  2.8-0,  2.7-0,  2.6.2-0,  2.6.1-3,  2.6.1-2,  2.6.1-1,  2.6.1-0,  2.6.0-2,  2.6.0-1,  2.6.0-0,  2.5.3-0,  2.5.2-0,  2.5-2,  2.5-1,  2.5-0,  2.2-1,  2.2-0,  1.0.0-1,  1.0.0-0

depends _openmp_mutex:

>=4.5

depends kraken2:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends python:

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 bracken

and update with::

   mamba update bracken

To create a new environment, run:

mamba create --name myenvname bracken

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/bracken:<tag>

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

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