CoolBox is an open-source, user-friendly toolkit for visual analysis of genomics data. It is highly compatible with the Python ecosystem and customizable with a well-designed user interface. It can bed used, for example, to produce high-quality genome track plots or fetch commonly used genomic data files with a Python script or command line, to explore genomic data interactively within Jupyter environment or web browser.

References:

• Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li and Gang Cao,
  CoolBox: a flexible toolkit for visual analysis of genomics data
  BMC Bioinformatics (2021) 22:489

• CoolBox Github page
• CoolBox Documentation

• Module Name: coolbox (see the modules page for more information)
• Unusual environment variables set
  • CB_HOME  installation directory
  • CB_BIN       executable directory
  • CB_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cig 3335 ~]$ module load coolbox
[+] Loading singularity  3.10.5  on cn3335
[+] Loading coolbox/0.3.8    
[user@cn3335 ~]$ mkdir /data/$USER/coolbox && cd /data/$USER/coolbox
[user@cn3335 ~]$ coolbox version
0.3.8
[user@cn3335 ~]$ coolbox --help
NAME
    coolbox - CoolBox Command Line Interface

SYNOPSIS
    coolbox COMMAND | 

DESCRIPTION
    You can use this cli to create coolbox browser instance,
    visualize your data directly in shell.

    example:

    1. Draw tracks within a genome range, save figure to a pdf file:

        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - plot test.pdf

    2. Generate a notebook and run jupyter to open browser:

        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - run_jupyter

    3. Run a independent web application.

        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - run_webapp

FLAGS
    --genome=GENOME
        Default: 'hg19'
    --genome_range=GENOME_RANGE
        Type: Optional[str]
        Default: None
    --genome_range2=GENOME_RANGE2
        Type: Optional[str]
        Default: None

COMMANDS
    COMMAND is one of the following:

     show_doc
       Print the document of specified Element type. For example: coolbox show_doc Cool
     version
       print coolbox version
(END)
:q
[user@cn3335 ~]$ cp $CB_DATA/* .
[user@cn3335 ~]$ coolbox add XAxis - \
                        add Cool ./cool_chr9_4000000_6000000.mcool - \
                        add Title "cool" - \
                        add BAMCov ./bam_chr9_4000000_6000000.bam - \
                        add Title "bam" - \
                        add BigWig ./bigwig_chr9_4000000_6000000.bw - \
                        add Title "bigwig" - \
                        goto "chr9:4000000-6000000" - \
                        plot ./test_coolbox.png  

Make sure you set up a graphical X11 connection.

[user@cn3335 ~]$ display ./test_coolbox.png

[user@cn3335 ~]$ exit
user@biowulf]$