Biopython

Description

!!Under development!!

From the Biopython Home Page: Biopython 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.


Biopython can be installed by using the Anaconda 2.7 python bundle or 3.6 miniconda bundle apps on the cluster. Alternatively, and preferably, you may want to install a local copy of miniconda. It you do not want to use your own version of miniconda, follow these directions to load and use the miniconda version of biopython:


module load apps/miniconda

python

#within python

from Bio.Seq import Seq

#do stuff...

exit()

 


To install a local copy of conda so you have more control and can install and update more to more recent modules:


#change to Miniconda3-latest-Linux-x86_64.sh if you prefer python 3.6

1) cd $HOME
2) wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
3) chmod +x Miniconda2-latest-Linux-x86_64.sh
4) ./Miniconda2-latest-Linux-x86_64.sh
5) export PATH=$HOME/miniconda2/bin:$PATH

#open a bash window
conda install biopython

 



Version

  • 1.69 (python 3.6)
  • 1.70 (python 2.7)
  • 1.71 (python 3.6 local copy)

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

  • NA


Documentation

Home Page, User Guides, and Manuals


Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Biopython to the IT Help Desk: rc-help@usf.edu