recipe cazy_webscraper

A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB.

Homepage:

https://github.com/HobnobMancer/cazy_webscraper

Documentation:

https://hobnobmancer.github.io/cazy_webscraper

License:

MIT / MIT

Recipe:

/cazy_webscraper/meta.yaml

Links:

doi: 10.1101/2022.12.02.518825

package cazy_webscraper

versions:

2.3.0.4-0,  2.3.0.3-0,  2.3.0.2-0,  2.3.0-0,  2.2.8-0,  2.2.7-0,  2.2.6-0,  2.2.2-0,  2.2.1-0, 

2.3.0.4-0,  2.3.0.3-0,  2.3.0.2-0,  2.3.0-0,  2.2.8-0,  2.2.7-0,  2.2.6-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.3.1-0,  1.0.2-0

depends beautifulsoup4:

depends biopython:

depends bioservices:

>=1.10.0

depends html5lib:

depends lxml:

depends mechanicalsoup:

depends numpy:

depends pandas:

depends python:

>=3.8

depends pyyaml:

depends requests:

depends saintbioutils:

>=0.0.25

depends sqlalchemy:

1.4.20

depends tqdm:

requirements:

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 cazy_webscraper

and update with::

   mamba update cazy_webscraper

To create a new environment, run:

mamba create --name myenvname cazy_webscraper

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/cazy_webscraper:<tag>

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

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