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

[C. Titus Brown]

On Sun, Jul 06, 2014 at 10:09:20PM -0500, Efraim Rodrigues wrote:
> When I try to run 'make test'. It looks like it calls a script which runs
> pip2. I guess I cannot change it.
> 
> Oh, do not feel sorry. You guys are willing to help and that's all that
> matters.

well, thanks ;)

You can do:

	ln <virtualenv>/bin/pip <virtualenv>/bin/pip2

where you replace <virtualenv> with the path to your virtualenv directory.

cheers,
--titus

> On Sun, Jul 6, 2014 at 10:01 PM, C. Titus Brown <ctb at msu.edu> wrote:
> 
> > 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
> >>
> >>
> >

-- 
C. Titus Brown, ctb at msu.edu