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 biopython:

>=1.81

depends pyhmmer:

>=0.11.0

depends python:

>=3.9

depends urllib3:

>=2.3.0

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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