recipe kofamscan

KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam

Homepage:

https://www.genome.jp/tools/kofamkoala/

License:

MIT License

Recipe:

/kofamscan/meta.yaml

Links:

doi: 10.1093/bioinformatics/btz859

KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.

package kofamscan

(downloads) docker_kofamscan

versions:

1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends hmmer:

>=3.1,<3.3.1|>=3.3.2

depends parallel:

depends ruby:

>=2.4

requirements:

additional platforms:

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 kofamscan

and update with::

   mamba update kofamscan

To create a new environment, run:

mamba create --name myenvname kofamscan

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/kofamscan:<tag>

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

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