Package Recipe 'genomepy'

recipe genomepy

Install and use genomes & gene annotations the easy way!

Homepage:: https://github.com/vanheeringen-lab/genomepy
Documentation:: https://vanheeringen-lab.github.io/genomepy
License:: MIT / MIT
Recipe:: /genomepy/meta.yaml

Install and use genomes & gene annotations the easy way!

package genomepy¶

Versions:

0.16.3-0, 0.16.2-1, 0.16.2-0, 0.16.1-2, 0.16.1-1, 0.16.1-0, 0.16.0-0, 0.15.0-0, 0.14.0-2,

0.16.3-0, 0.16.2-1, 0.16.2-0, 0.16.1-2, 0.16.1-1, 0.16.1-0, 0.16.0-0, 0.15.0-0, 0.14.0-2, 0.14.0-1, 0.14.0-0, 0.13.1-0, 0.13.0-0, 0.12.0-0, 0.11.1-0, 0.11.0-0, 0.10.0-0, 0.9.3-0, 0.9.2-0, 0.9.1-0, 0.9.0-0, 0.8.4-0, 0.8.3-0, 0.8.2-0, 0.8.1-1, 0.8.1-0, 0.7.2-0, 0.7.1-0, 0.7.0-0, 0.6.1-0, 0.6.0-0, 0.5.5-1, 0.5.5-0, 0.5.4-1, 0.5.4-0, 0.5.2-2, 0.5.2-1, 0.5.1-0, 0.5.0-0, 0.4.0-0, 0.3.1-0

Depends:

on appdirs
on biopython >=1.73
on click
on colorama
on diskcache
on filelock >=3.5
on htslib >=1.11
on loguru
on mygene
on mysql <=8.4
on mysql-connector-python <=8.4
on numpy
on pandas
on pyfaidx >=0.7.2.1
on python >=3.9
on pyyaml
on requests
on tqdm >=4.51
on ucsc-bedtogenepred
on ucsc-genepredtobed
on ucsc-genepredtogtf
on ucsc-gff3togenepred
on ucsc-gtftogenepred

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 genomepy

to add into an existing workspace instead, run:

pixi add genomepy

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 genomepy

Alternatively, to install into a new environment, run:

conda create -n envname genomepy

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/genomepy:<tag>

(see genomepy/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/genomepy/README.html)