recipe pubgator

A lightweight python wrapper for the PubTator3 API. PubGator allows to easily interact with the PubTator API. It provides a simple interface to search for publications, retrieve full annotations, and find entities and relations. It also automatically handles pagination and rate limiting.

Homepage:

https://github.com/koesterlab/pubgator

License:

MIT

Recipe:

/pubgator/meta.yaml

package pubgator

versions:

0.3.0-0,  0.2.0-0

depends bioc:

>=2.1,<3

depends httpx:

>=0.28.1,<0.29

depends python:

>=3.11

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 pubgator

and update with::

   mamba update pubgator

To create a new environment, run:

mamba create --name myenvname pubgator

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/pubgator:<tag>

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

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