recipe dbcan

Standalone version of dbCAN annotation tool for automated CAZyme annotation.

Homepage:

https://bcb.unl.edu/dbCAN2

Documentation:

https://run-dbcan-new.readthedocs.io/en/latest/

Developer docs:

https://github.com/bcb-unl/run_dbcan_new

License:

GPL3 / GPL-3.0-or-later

Recipe:

/dbcan/meta.yaml

Links:

doi: 10.1093/nar/gkx894, doi: 10.1093/nar/gky418, doi: 10.1093/nar/gkad328, biotools: dbcan2

package dbcan

versions:

5.0.0-0,  4.1.4-1,  4.1.4-0,  4.1.3-0,  4.1.2-0,  4.1.1-0,  4.1.0-0,  4.0.0-0,  3.0.7-0, 

5.0.0-0,  4.1.4-1,  4.1.4-0,  4.1.3-0,  4.1.2-0,  4.1.1-0,  4.1.0-0,  4.0.0-0,  3.0.7-0,  3.0.6-0

depends bcbio-gff:

depends biopython:

depends diamond:

depends matplotlib-base:

depends natsort:

depends numpy:

>1.19

depends openpyxl:

depends pandas:

depends psutil:

depends pycirclize:

depends pyhmmer:

depends pyrodigal:

depends pysam:

depends python:

>=3.10

depends requests:

depends rich-click:

depends scipy:

depends seaborn:

depends session-info:

depends tqdm:

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 dbcan

and update with::

   mamba update dbcan

To create a new environment, run:

mamba create --name myenvname dbcan

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/dbcan:<tag>

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

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