Package Recipe 'cazy_webscraper'

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:

on beautifulsoup4
on biopython
on bioservices >=1.10.0
on html5lib
on lxml
on mechanicalsoup
on numpy
on pandas
on python >=3.8
on pyyaml
on requests
on saintbioutils >=0.0.25
on sqlalchemy 1.4.20
on tqdm

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 cazy_webscraper

to add into an existing workspace instead, run:

pixi add cazy_webscraper

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 cazy_webscraper

Alternatively, to install into a new environment, run:

conda create -n envname cazy_webscraper

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/cazy_webscraper:<tag>

(see cazy_webscraper/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/cazy_webscraper/README.html)