There is a newer version of BiopythonBiopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
Accessing Biopython 1.73-foss-2019a
To load the module for Biopython 1.73-foss-2019a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load Biopython/1.73-foss-2019a
There is a GPU enabled version of this module: Biopython 1.73-fosscuda-2019a
BEAR Apps Version
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.
For more information visit the Biopython website.
This version of Biopython has a direct dependency on: foss/2019a Python/2.7.15-GCCcore-8.2.0 Python/3.7.2-GCCcore-8.2.0 SciPy-bundle/2019.03-foss-2019a
This version of Biopython 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 Biopython.
This version of Biopython is a direct dependent of: SpliceAI/1.3-foss-2019a-Python-3.7.2 WhatsHap/0.18-foss-2019a-Python-3.7.2
These versions of Biopython 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 22nd July 2019