recipe dbcanlight

A lightweight CAZyme annotation tool

Homepage:

https://github.com/chtsai0105/dbcanlight

Documentation:

https://github.com/chtsai0105/dbcanlight/blob/v1.1.0/README.md

License:

MIT / MIT

Recipe:

/dbcanlight/meta.yaml

Dbcanlight is a lightweight rewrite of a widely used CAZyme annotation tool run_dbcan. It uses pyhmmer, a Cython bindings to HMMER3, to instead the cli version of HMMER3 suite as the backend for the search processes, which improves the multithreading performance. In addition, it also solves the inconvenience process in the run dbcan that the large sequence file required manual splitting beforehand.

The main program dbcanlight comprises 3 modules - build, search and conclude. The build module help to download the required databases from dbcan website; the search module searches against protein HMM, substrate HMM or diamond databases and reports the hits separately; and the conclude module gathers all the results made by each module and provides a brief overview. The output of dbcanlight is resemble to run_dbcan with slight cleanup. Run_dbcan output the same substrate several times for a gene that hits multiple profiles with the same substrate; in dbcanlight we only report it once.

Dbcanlight only re-implemented the core features of run_dbcan, that is searching for CAZyme and substrate matches by hmmer/diamond/dbcansub. Submodules like signalP, CGCFinder, etc. are not implemented.

package dbcanlight

(downloads) docker_dbcanlight

versions:

1.1.0-0,  1.0.2-0,  1.0.1-0,  1.0.0-0

depends biopython:

>=1.81

depends importlib-metadata:

depends pyhmmer:

>=0.10.4

depends python:

>=3.7

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 dbcanlight

and update with::

   mamba update dbcanlight

To create a new environment, run:

mamba create --name myenvname dbcanlight

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/dbcanlight:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/dbcanlight/README.html)