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Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

For more information, please check its website: and its home page on Github.


  • 0.8.11


  • cooler

  • python

  • python3


You can load the modules by:

module load biocontainers
module load Cooler

Interactive job

To run Cooler interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers cooler
(base) UserID@bell-a008:~ $ python
Python 3.9.7 |  packaged by conda-forge |  (default, Sep 29 2021, 19:20:46)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cooler

Batch job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Cooler batch jobs on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=cooler
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cooler

cooler info data/
cooler info -f bin-size data/
cooler info -m data/
cooler tree data/
cooler attrs data/