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

Efraim Rodrigues efraimnaassom at gmail.com
Sun Jul 6 19:53:10 PDT 2014


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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