BEAR Applications

pybedtools 0.8.1-foss-2019b

There is a newer version of pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Accessing pybedtools 0.8.1-foss-2019b

To load the module for pybedtools 0.8.1-foss-2019b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load pybedtools/0.8.1-foss-2019b

BEAR Apps Version

2019b

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

• BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
• BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the pybedtools website.

Dependencies

This version of pybedtools has a direct dependency on: BEDTools/2.29.2-GCC-8.3.0 foss/2019b Pysam/0.15.3-GCC-8.3.0 Python/2.7.16-GCCcore-8.3.0 Python/3.7.4-GCCcore-8.3.0

This version of pybedtools is compatible with multiple vesions of Python. At any time, only one of the versions of Python can be active and the desired version of Python should be loaded before loading this version of pybedtools.

Required By

This version of pybedtools is a direct dependent of: biofluff/2.1.4-foss-2019b-Python-2.7.16 biofluff/3.0.3-foss-2019b-Python-3.7.4

Other Versions

These versions of pybedtools are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 23rd September 2020