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

[C. Titus Brown]

Just try pip (not pip2). Sorry for all the mess :(

> On Jul 6, 2014, at 7:53 PM, Efraim Rodrigues <efraimnaassom at gmail.com> wrote:
> 
> Hi. Thanks for your response.
> 
> It looks like the we are supposed to choose the version of the virtualenv. I found all the versions here https://pypi.python.org/packages/source/v/virtualenv/ so I am followed these steps using the newest version of the virtualen, in this case, I believe that is, https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.tar.gz
> 
> Anyway, I ran all the tests and it still returns the same problem.
> 
>  make test
> pip2 install --user nose || pip2 install nose
> /bin/sh: pip2: command not found
> /bin/sh: pip2: command not found
> make: *** [test] Error 127
> 
> In fact, there is no pip2 inside khmerEnv. I can just see these files:
> 
> activate      activate.fish     easy_install      pip      python   python2.7
> activate.csh  activate_this.py  easy_install-2.7  pip-2.7  python2
> 
> Should I try another version of virutalenv or perhaps another similar tool?
> 
> Thank y'all for trying to help me.
> 
> 
>> On Sun, Jul 6, 2014 at 5:25 PM, C. Titus Brown <ctb at msu.edu> wrote:
>> 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
> 
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