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

[Michael R. Crusoe]

The lack of `pip2` when installed this way is fixed in the latest
virtualenv release (1.11.6):

```
curl -O
https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz
tar xzf virtualenv*
python2.7 virtualenv*/virtualenv.py khmerEnv
source khmerEnv/bin/activate
pip2 --version
```


On Sun, Jul 6, 2014 at 11:11 PM, C. Titus Brown <ctb at msu.edu> wrote:

> 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
>
> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer
>



-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe
<http://twitter.com/biocrusoe>
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