cooler
Link to section 'Introduction' of 'cooler' Introduction
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: https://biocontainers.pro/tools/cooler and its home page on Github.
Link to section 'Versions' of 'cooler' Versions
- 0.8.11
Link to section 'Commands' of 'cooler' Commands
- cooler
- python
- python3
Link to section 'Module' of 'cooler' Module
You can load the modules by:
module load biocontainers
module load Cooler
Link to section 'Interactive job' of '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
Link to section 'Batch job' of '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:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cooler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cooler
cooler info data/Rao2014-GM12878-MboI-allreps-filtered.1000kb.cool
cooler info -f bin-size data/Rao2014-GM12878-MboI-allreps-filtered.1000kb.cool
cooler info -m data/Rao2014-GM12878-MboI-allreps-filtered.1000kb.cool
cooler tree data/Rao2014-GM12878-MboI-allreps-filtered.1000kb.cool
cooler attrs data/Rao2014-GM12878-MboI-allreps-filtered.1000kb.cool