- recipe recognizer
A tool for domain based annotation with the COG database
- Homepage:
- Documentation:
https://github.com/iquasere/reCOGnizer/blob/master/README.md
- License:
BSD / BSD-3-Clause
- Recipe:
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¶
- 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:
on blast
>=2.12on krona
on lxml
on openpyxl
on pandas
on python
on requests
on tqdm
on wget
on xlsxwriter
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install recognizer
to add into an existing workspace instead, run:
pixi add recognizer
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install recognizer
Alternatively, to install into a new environment, run:
conda create -n envname recognizer
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/recognizer:<tag>
(see recognizer/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/recognizer/README.html)
