Package Recipe 'coolbox'

recipe coolbox

Jupyter notebook based genomic data visulization toolkit.

Homepage:: https://github.com/GangCaoLab/CoolBox
License:: GPL3 / GPL-3.0-or-later
Recipe:: /coolbox/meta.yaml

package coolbox¶

Versions:

0.4.0-0, 0.3.9-0, 0.3.8-0, 0.3.7-1, 0.3.7-0, 0.3.6-0, 0.3.5-0, 0.3.4-0, 0.3.3-0,

0.4.0-0, 0.3.9-0, 0.3.8-0, 0.3.7-1, 0.3.7-0, 0.3.6-0, 0.3.5-0, 0.3.4-0, 0.3.3-0, 0.3.1-0, 0.3.0-0, 0.2.2-0, 0.2.1-0

Depends:

on cooler >=0.8.10
on dna_features_viewer
on fire
on h5py
on htslib
on intervaltree
on ipywidgets >=7.5.1
on jupyter >=1.0.0
on matplotlib-base >=3.1.1
on nbformat
on numpy
on numpydoc
on pairix
on pandas >=1.0.0
on pybbi
on python >=3.7
on samtools >=1.10
on scipy >=1.0.0
on statsmodels
on svgutils
on voila

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 coolbox

to add into an existing workspace instead, run:

pixi add coolbox

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 coolbox

Alternatively, to install into a new environment, run:

conda create -n envname coolbox

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/coolbox:<tag>

(see coolbox/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/coolbox/README.html)