[khmer] normalize-by-median.py - IOError: [Errno 30] Read-only file system:

[C. Titus Brown]

On Sat, Jul 05, 2014 at 03:01:47PM -0500, Efraim Rodrigues wrote:
> Hi everyone,
> 
> Actually, when I tried to install by running 'make test', it returned the
> following message:
> 
> pip2 install --user nose || pip2 install nose
> /bin/sh: pip2: command not found
> /bin/sh: pip2: command not found
> 
> 
> Even though we have python/2.7 installed, It looks like my system has
> python/2.6 as default. Hence, in order to install 'khmer', I followed these
> steps:
> 
> module load python/2.7
> 
> python setup.py install --user
> 
> Apparently, it worked to install it locally, however I'm not sure about any
> additional file or module.

OK, I would suggest running the tests inside of virtualenv.  try:

curl -O https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.x.y.tar.gz
tar xzf virtualenv*
cd virtualenv-*; python2.7 virtualenv.py ../khmerEnv; cd ..
source khmerEnv/bin/activate

and then 'make test'.

thanks!
--titus