recipe kraken

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

Homepage:

http://ccb.jhu.edu/software/kraken/

License:

GPLv3

Recipe:

/kraken/meta.yaml

Links:

biotools: kraken, doi: 10.1186/gb-2014-15-3-r46

package kraken

versions:

1.1.1-9,  1.1.1-8,  1.1.1-7,  1.1.1-6,  1.1.1-5,  1.1.1-4,  1.1.1-3,  1.1.1-2,  1.1.1-0, 

1.1.1-9,  1.1.1-8,  1.1.1-7,  1.1.1-6,  1.1.1-5,  1.1.1-4,  1.1.1-3,  1.1.1-2,  1.1.1-0,  1.1-2,  1.1-1,  1.1-0,  1.0-0,  0.10.6_eaf8fb68-4,  0.10.6_eaf8fb68-3,  0.10.6_eaf8fb68-2,  0.10.6_eaf8fb68-1,  0.10.6_eaf8fb68-0,  0.10.5beta-2,  0.10.5beta-0

depends kmer-jellyfish:

1.*

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends rsync:

depends tar:

depends wget:

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 kraken

and update with::

   mamba update kraken

To create a new environment, run:

mamba create --name myenvname kraken

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/kraken:<tag>

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

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