recipe kraken2

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Homepage:

https://ccb.jhu.edu/software/kraken2

Documentation:

https://github.com/DerrickWood/kraken2/blob/v2.1.6/docs/MANUAL.markdown

Developer docs:

https://github.com/DerrickWood/kraken2

License:

GPL3 / GPL-3.0-or-later

Recipe:

/kraken2/meta.yaml

Links:

biotools: kraken2, usegalaxy-eu: kraken2, doi: 10.1186/gb-2014-15-3-r46, doi: 10.1186/s13059-019-1891-0

package kraken2

versions:

2.14-0,  2.1.6-0,  2.1.5-0,  2.1.3-4,  2.1.3-3,  2.1.3-2,  2.1.3-1,  2.1.3-0,  2.1.2-4, 

2.14-0,  2.1.6-0,  2.1.5-0,  2.1.3-4,  2.1.3-3,  2.1.3-2,  2.1.3-1,  2.1.3-0,  2.1.2-4,  2.1.2-3,  2.1.2-2,  2.1.2-1,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.1.0-0,  2.0.9beta-0,  2.0.8_beta-2,  2.0.8_beta-1,  2.0.8_beta-0,  2.0.7_beta-3,  2.0.7_beta-2,  2.0.7_beta-1,  2.0.7_beta-0

depends _openmp_mutex:

>=4.5

depends blast:

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends python:

depends rsync:

depends tar:

depends wget:

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 kraken2

and update with::

   mamba update kraken2

To create a new environment, run:

mamba create --name myenvname kraken2

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/kraken2:<tag>

(see `kraken2/tags`_ for valid values for ``<tag>``)

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