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

[Michael R. Crusoe]

Thank you tim for your email.

It should work under Python2.6.

Note: your pip install error message indicates that you weren't using the
virtualenv. Using the recommended install method you will have to activate
the virtualenv each time you login and want to use khmer.

On Mon, Nov 17, 2014, 16:34 Timothy Driscoll <bioinformatics451 at gmail.com>
wrote:

> 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/
>
>
>
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