[khmer] khmer install on RHE6 - will it work under Python 2.6?

[Timothy Driscoll]

hello,

I am trying to set up khmer in a RedHat Enterprise environment, following the instructions here:

<http://khmer.readthedocs.org/en/latest/user/install.html>

khmer is said to require Python 2.7+, and RHE6 has Python 2.6 as default, so first I installed 2.7.5 as a Software Collection and permanently enabled it - successfully, it would seem:

$ python -V
Python 2.7.5

then I created a virtualenv, activated it, and ran pip install khmer. that failed:


creating /usr/lib64/python2.6/site-packages/khmer
error: could not create '/usr/lib64/python2.6/site-packages/khmer': Permission denied


but I fixed it with sudo. that install succeeded, but it looks like it installed it under python 2.6. running nosetests:


$ nosetests khmer --attr '!known_failing'
E
======================================================================
ERROR: Failure: ImportError (No module named khmer)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/nose/loader.py", line 402, in loadTestsFromName
    module = resolve_name(addr.module)
  File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/nose/util.py", line 311, in resolve_name
    module = __import__('.'.join(parts_copy))
ImportError: No module named khmer

----------------------------------------------------------------------
Ran 1 test in 0.001s

FAILED (errors=1)


will khmer run ok under Python 2.6? if not, is there a work-around to install it in Python 2.7 for RH? I can't overwrite the default Python, and I'm conversant with linux but not an expert.


thanks in advance for any help,

tim
-- 
timothy driscoll, phd
twitter @MobileElement
skype   bioinformatics451

natural sciences 333
department of biology
western carolina university
cullowhee nc 28723

http://TheMobileElements.blogspot.com/