pybigwig
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'pybigwig' Versions
- 0.3.18
Link to section 'Commands' of 'pybigwig' Commands
- python
- python3
Link to section 'Module' of 'pybigwig' Module
You can load the modules by:
module load biocontainers
module load pybigwig
Link to section 'Interactive job' of '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")
Link to section 'Batch job' of 'pybigwig' 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 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