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

[Timothy Driscoll]

thanks Michael. I'll give it a go under 2.6.

just curious: any idea why it wasn't using the virtualenv? I'm pretty sure I ran pip install from within one (see below). (I understand if this list is not the best venue for this question; I'm just curious to know what I messed up.)


[17-Mon 16:17:50] tpdriscoll at firefly:~
$ source venv/bin/activate

[17-Mon 16:18:28](venv) tpdriscoll at firefly:~
$ pip2 install khmer

Downloading/unpacking khmer
  Downloading khmer-1.1.tar.gz (3.6MB): 3.6MB downloaded
  Running setup.py (path:/tmp/pip_build_tpdriscoll/khmer/setup.py) egg_info for package khmer
    warning: no previously-included files found matching 'third-party/zlib/Makefile'
    warning: no previously-included files found matching 'third-party/zlib/zconf.h'
    warning: no previously-included files matching '*.orig' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
Downloading/unpacking screed>=0.7.1 (from khmer)
  Downloading screed-0.7.1.tar.gz
  Running setup.py (path:/tmp/pip_build_tpdriscoll/screed/setup.py) egg_info for package screed
Downloading/unpacking argparse>=1.2.1 (from khmer)
  Downloading argparse-1.2.2-py2.py3-none-any.whl
Installing collected packages: khmer, screed, argparse
  Running setup.py install for khmer
    got version from file /tmp/pip_build_tpdriscoll/khmer/khmer/_version.py {'version': '1.1', 'full': '1fe98c92b5a9b3f46a5f4f05cd35d3229ce2ff0a'}
    warning: no previously-included files found matching 'third-party/zlib/Makefile'
    warning: no previously-included files found matching 'third-party/zlib/zconf.h'
    warning: no previously-included files matching '*.orig' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    bash -c cd third-party/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC
...



-- 
timothy driscoll, phd
twitter @MobileElement
skype   bioinformatics451

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

http://TheMobileElements.blogspot.com/


On Nov 17, 2014, at 4:42 PM, Michael R. Crusoe <mcrusoe at msu.edu> wrote:

> 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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