Installation & Usage¶

Install CoolBox¶

Recommend use conda to manage environments.

You can install from the bioconda channel:

$ conda install -c bioconda coolbox

Or install from the source code, by this way you can use the latest updated features:

$ git clone https://github.com/GangCaoLab/CoolBox.git
$ cd CoolBox
$ conda env create --file environment.yml
$ conda activate coolbox
$ python setup.py install

Another way is install from PyPI. But you should ensure these dependency is installed.

$ pip install coolbox

After installation, you should enable ipywidgets to use the browser in Jupyter notebook:

$ jupyter nbextension enable --py widgetsnbextension

Usage¶

CoolBox can be use in two ways. Directly using its Python API or using the command line interface.

API¶

User can import coolbox in Jupyter notebook to draw figures or compose a Browser object to interactively explore their genomic data.

browser

For this purpose, you can reference this Quickstart (API) page. Or just import coolbox as a Python plot package use in their own plot script.

CLI¶

Command line users can use CoolBox in a more convenient way. They can directly draw genomic track plot or compose browser by simple command line:

fig_CLI

For Windows Users¶

Currently, CoolBox cannot be run natively on Windows. But you can use the WSL(Windows Subsystem for Linux) to run it. See this

Or, you can choose to use docker on Windows.

Docker¶

Pull the CoolBox docker image:

$ docker pull nanguage/coolbox

Run a container, with mount current directory in file system to the ‘/data’ in the container. And binding the container port 8888 (jupyter default port) to the host port 9000:

$ docker run -ti -v $(pwd):/data -p 9000:8888 nanguage/coolbox:latest

Then run jupyter notebook in the container:

$ jupyter notebook --ip=0.0.0.0 --allow-root
## will print the token here

Then open http://127.0.0.1:9000/ with your browser, and type the token printed in the console.