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 adjusttext:

depends biopython:

>=1.64

depends fisher:

>=0.1.5

depends hmmlearn:

0.2.2

depends htseq:

depends joblib:

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends logomaker:

depends matplotlib-base:

>=1.1.0

depends matplotlib-venn:

depends moods:

>=1.9.4.1

depends mpmath:

depends natsort:

depends numpy:

>=1.4.0

depends pandas:

depends pybigwig:

depends pysam:

>=0.20.0

depends python:

>=3.7,<3.8.0a0

depends python_abi:

3.7.* *_cp37m

depends pyx:

depends scikit-learn:

>=0.19.0

depends scipy:

>=1.0.0

depends seaborn:

depends ucsc-bedgraphtobigwig:

depends ucsc-bedtobigbed:

depends ucsc-bigbedtobed:

depends ucsc-bigwigmerge:

depends ucsc-wigtobigwig:

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 rgt

and update with::

   mamba update rgt

To create a new environment, run:

mamba create --name myenvname rgt

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/rgt:<tag>

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

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