recipe gget

gget enables efficient querying of genomic databases.

Homepage:

https://github.com/pachterlab/gget

Documentation:

https://pachterlab.github.io/gget

License:

BSD / BSD-2-Clause

Recipe:

/gget/meta.yaml

Links:

doi: 10.1093/bioinformatics/btac836

gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.

package gget

versions:

0.29.0-0,  0.28.6-0,  0.28.5-0,  0.28.4-0,  0.28.3-0,  0.28.2-0,  0.28.1-0,  0.27.9-0,  0.27.8-0, 

0.29.0-0,  0.28.6-0,  0.28.5-0,  0.28.4-0,  0.28.3-0,  0.28.2-0,  0.28.1-0,  0.27.9-0,  0.27.8-0,  0.27.7-0,  0.27.5-0,  0.27.4-0,  0.27.3-0,  0.27.2-2,  0.27.2-1,  0.27.2-0,  0.27.0-0,  0.3.13-0,  0.3.12-0,  0.3.11-0,  0.3.10-0,  0.3.9-0,  0.3.7-0,  0.3.5-0,  0.2.7-0,  0.2.6-0,  0.2.5-0,  0.2.3-0,  0.2.2-0,  0.2.1-0,  0.2.0-0,  0.1.2-0,  0.1.1-0,  0.1.0-0,  0.0.24-0

depends bs4:

>=4.10.0

depends curl:

depends ipython:

depends ipywidgets:

depends lxml:

depends matplotlib-base:

depends mysql-connector-python:

>=8.0.32

depends numpy:

>=1.17.2

depends openai:

depends openmm:

7.5.1

depends pandas:

>=1.0.0

depends py3dmol:

>=1.8.0

depends python:

>=3.7

depends requests:

>=2.22.0

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 gget

and update with::

   mamba update gget

To create a new environment, run:

mamba create --name myenvname gget

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/gget:<tag>

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

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