Package Recipe 'dbcanlight'

recipe dbcanlight

A lightweight CAZyme annotation tool

Homepage:: https://github.com/chtsai0105/dbcanlight
Documentation:: https://github.com/chtsai0105/dbcanlight/blob/v1.1.1/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 binding to HMMER3, in place of the HMMER3 CLI suite as the backend for search processes, improving multithreading performance. In addition, it removes a limitation in run_dbcan that required manual splitting of large sequence files beforehand.

The main program dbcanlight comprises three 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 summary. The output format closely resembles that of run_dbcan, with minor cleanup. For example, run_dbcan may report the same substrate multiple times for a gene matching several profiles with that substrate, whereas dbcanlight reports it only once.

Dbcanlight only reimplemented 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¶

Versions:

1.1.1-0, 1.1.0-0, 1.0.2-0, 1.0.1-0, 1.0.0-0

Depends:

on biopython >=1.81
on pyhmmer >=0.11.0
on python >=3.9
on urllib3 >=2.3.0

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 dbcanlight

to add into an existing workspace instead, run:

pixi add dbcanlight

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 dbcanlight

Alternatively, to install into a new environment, run:

conda create -n envname dbcanlight

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/dbcanlight:<tag>

(see dbcanlight/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:

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