recipe varpubs

Tool for finding PubMed evidence on genetic variants and generating LLM-based summaries

Homepage:

https://github.com/koesterlab/varpubs

License:

MIT

Recipe:

/varpubs/meta.yaml

package varpubs

versions:

0.2.1-0,  0.2.0-0,  0.1.2-0,  0.1.1-0

depends biopython:

>=1.85,<2

depends cyvcf2:

>=0.31.1,<0.32

depends duckdb:

>=1.2.1,<2

depends duckdb-engine:

>=0.15.0,<0.16

depends openai:

>=1.97.0,<2

depends python:

>=3.11

depends simple-parsing:

depends sqlalchemy:

>=2.0.39,<3

depends sqlmodel:

>=0.0.24,<0.0.25

depends typed-argument-parser:

>=1.10.1,<2

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 varpubs

and update with::

   mamba update varpubs

To create a new environment, run:

mamba create --name myenvname varpubs

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/varpubs:<tag>

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

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Link to this page

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