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I have attempted to install biopython for python2.7 on a cluster of machines.

I have a tonne of scripts that are written in python2.7 and I need to use biopython, but the refactoring of the scripts is more hassle than it is worth - so I thought it would be easier to use an install workaround.

pip install python2 biopython

and

pip install python2.7 biopython

and all variations of these calls do nothing.

They tell me everything is satisfied because there is an installation of biopython for python3.4.

Does anyone know this installation command?

urema
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1 Answers1

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Since version 0.8 you can use the following:

$ pip-2.5 install package
$ pip-2.6 install package
$ pip-2.7 install package

Also see this question: pip: dealing with multiple Python versions?

  • Sorry I then tried 'pip2.7 install biopython' - and I receive that the requirements are satisfied - then i try to import Bio and it fails – urema Sep 26 '17 at 08:56
  • I am... I dont know what else I can say. On my local machine these commands work perfectly and I have biopython working - on a cluster machine they dont execute – urema Sep 26 '17 at 09:04
  • did you try reinstall the package –  Sep 26 '17 at 09:42
  • can you try: `python -m pip install biopython`. Maybe this installs it to whatever python you are using. –  Sep 26 '17 at 10:16
  • andi - thanks for your input. However I dont want to install biopython for my current version as my original post states - I want to install biopython to work an earlier version of python as I have hundreds of scripts (thousands and thousands of lines of code) that are incompatible with python3.2 so I want to ensure that biopython runs well for python2.7 (as it is meant to be supported with python2.7 anyway) – urema Sep 26 '17 at 10:23
  • Biopython for Python2.7 fails miserably even though the biopython requirements are satisfied for python2.7 – urema Sep 26 '17 at 10:24
  • well, than I think you want to run `python2.7 -m pip install biopython` –  Sep 26 '17 at 10:24
  • Okay. Than I think I cannot do much more based on the provided information :( Sorry. –  Sep 26 '17 at 10:24
  • python2.7 -m pip install biopython - does nothing for me either – urema Sep 26 '17 at 10:27
  • Okay cheers for your effort anyway - so as far as I am concerned and the effort of trying to smash my face against this for weeks and weeks - PYTHON2.7 DOES NOT IN ANY WAY SUPPORT BIOPYTHON - despite what the literature says – urema Sep 26 '17 at 10:27
  • I have to disagree. For me it works perfectly fine. I am still pretty sure you do not install biopython correctly :( –  Sep 26 '17 at 11:27
  • Biopython wont install that is the issue sir lol - I know it wont install. Hence why I asked this question about how to install biopython............I am told that biopython is supported automatically with python2.7 - and I am saying that this is not true - I have a version of python2.7 for which biopython is not supported automatically, and considering we only need one example of where something doesnt work for it to be false, then I cannot rightly say that biopython is supported by python2,7 as my python 2,7 has no such thing – urema Sep 26 '17 at 11:45
  • No offense was intended. My apologies. –  Sep 26 '17 at 11:50
  • No andi.... none taken what so ever. I was merely attempting to clarify my position for you. I appreciate your effort of even reading this problem, as well as all your input. – urema Sep 26 '17 at 12:06