Package Recipe 'rgt'

recipe rgt

Toolkit to perform regulatory genomics data analysis

Homepage:: http://www.regulatory-genomics.org
Documentation:: http://www.regulatory-genomics.org/rgt/tutorial/
Developer docs:: https://github.com/CostaLab/reg-gen
License:: GPL / GPL-3.0-or-later
Recipe:: /rgt/meta.yaml

package rgt¶

Versions:

1.0.2-0, 1.0.1-0, 1.0.0-0, 0.12.3-3, 0.12.3-2, 0.12.3-1, 0.12.3-0, 0.12.2-0, 0.11.4-2,

1.0.2-0, 1.0.1-0, 1.0.0-0, 0.12.3-3, 0.12.3-2, 0.12.3-1, 0.12.3-0, 0.12.2-0, 0.11.4-2, 0.11.4-1, 0.11.4-0

Depends:

on adjusttext
on biopython >=1.64
on fisher >=0.1.5
on hmmlearn 0.2.2
on htseq
on joblib
on libgcc-ng >=12
on libzlib >=1.2.13,<1.3.0a0
on logomaker
on matplotlib-base >=1.1.0
on matplotlib-venn
on moods >=1.9.4.1
on mpmath
on natsort
on numpy >=1.4.0
on pandas
on pybigwig
on pysam >=0.20.0
on python >=3.7,<3.8.0a0
on python_abi 3.7.* *_cp37m
on pyx
on scikit-learn >=0.19.0
on scipy >=1.0.0
on seaborn
on ucsc-bedgraphtobigwig
on ucsc-bedtobigbed
on ucsc-bigbedtobed
on ucsc-bigwigmerge
on ucsc-wigtobigwig

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 rgt

to add into an existing workspace instead, run:

pixi add rgt

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 rgt

Alternatively, to install into a new environment, run:

conda create -n envname rgt

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/rgt:<tag>

(see rgt/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/rgt/README.html)