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

[Michael R. Crusoe]

If you could include the exact command (with parameters) that is causing
the problem and which directory you run it in that would be useful.


On Mon, Jul 7, 2014 at 12:09 AM, Efraim Rodrigues <efraimnaassom at gmail.com>
wrote:

> Alright! Awesome!
>
> I am sorry guys, I did not see that the newest version was the 1.11.6.
>
> Well, 'make test' worked and the result was 'OK'.
>
> I'm going back to the initial problem which was error  IOError: [Errno
> 30] Read-only file system: . I'll try to run it again and I'll let you guys
> know about the result.
>
> Thanks one more time and I'm sorry about not getting the newest version.
>
>
> On Sun, Jul 6, 2014 at 11:01 PM, Michael R. Crusoe <mcrusoe at msu.edu>
> wrote:
>
>> 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>
>>
>
>


-- 
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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