Pybigwig

Introduction

Pybigwig is a python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

For more information, please check its website: https://biocontainers.pro/tools/pybigwig and its home page on Github.

Versions

• 0.3.18

Commands

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load pybigwig

Interactive job

To run pybigwig 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 pybigwig
(base) UserID@bell-a008:~ $ python
Python 3.6.15 |  packaged by conda-forge |  (default, Dec  3 2021, 18:49:41)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyBigWig
>>> bw = pyBigWig.open("test/test.bw")

Batch job

Warning

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 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=pybigwig
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pybigwig

python script.py