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/$USER/coolbox &&iamp; cd /data/$USER/coolbox
[user@cn3335 ~]$ cp $CB_DATA/* .
[user@cn3335 ~]$ wget https://github.com/GangCaoLab/CoolBox/archive/refs/tags/0.3.8.tar.gz
[user@cn3335 ~]$ tar -zxf 0.3.8.tar.gz &&iamp; rm -f 0.3.8.tar.gz &&iamp; cd CoolBox-0.3.8
[user@cn3335 ~]$ scripts/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 -  goto "chr9:4000000-6000000" -  plot test_coolbox.png

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