recipe recognizer

A tool for domain based annotation with the COG database

Homepage:

https://github.com/iquasere/reCOGnizer

Documentation:

https://github.com/iquasere/reCOGnizer/blob/master/README.md

License:

BSD / BSD-3-Clause

Recipe:

/recognizer/meta.yaml

reCOGnizer performs domain based annotation with RPS-BLAST, using Hidden Markov Models (HMM) from COG database. It rebuilds COG database for multithreaded annotation, organizes information regarding COG IDs and respective categories, obtains EC numbers using resources from the eggNOG database and organizes all this information into TSV and EXCEL files for easy handling by users or pipelines. It also produces a Krona plot representing the quantification of COG functions identified.

package recognizer

(downloads) docker_recognizer

versions:
1.11.1-0,  1.11.0-0,  1.10.1-0,  1.10.0-0,  1.9.4-0,  1.9.3-0,  1.9.2-0,  1.9.1-0,  1.9.0-0, 

1.11.1-0,  1.11.0-0,  1.10.1-0,  1.10.0-0,  1.9.4-0,  1.9.3-0,  1.9.2-0,  1.9.1-0,  1.9.0-0,  1.8.3-0,  1.8.2-0,  1.8.1-0,  1.8.0-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.5-0,  1.6.4-0,  1.6.3-0,  1.6.2-0,  1.6.1-0,  1.6.0-0,  1.5.3-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.10-0,  1.4.9-0,  1.4.8-0,  1.4.7-0,  1.4.6-0,  1.4.5-0,  1.4.4-1,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.5-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0

depends blast:

>=2.12

depends krona:

depends lxml:

depends openpyxl:

depends pandas:

depends python:

depends requests:

depends tqdm:

depends wget:

depends xlsxwriter:

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 recognizer

and update with::

   mamba update recognizer

To create a new environment, run:

mamba create --name myenvname recognizer

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/recognizer:<tag>

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

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