Re: [Biskit-general] Problem in Installing Biskit
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Re: [Biskit-general] Problem in Installing Biskit
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From: Raik G. <rai...@cr...> - 2012-01-04 14:12:16
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Hi Amir,
that looks good then! Don't worry too much about the PVM error
message. It will be rather difficult to get PVM installed on a windows
system anyway. It can already be quite painful even on Linux. If you
are annoyed by it, simply edit Biskit/PVM/__init__.py and switch off
the message by commenting out:
if not pvm_installed:
EHandler.warning('Could not import PVM (Parallel Virtual Machine) modules.'+
' Please check that PVM and pypvm are installed!\n'+
'\tParallelisation is not available.')
Biskit also works very well without Biggles but several modules use
Biggles for making nice plots so it would be nice to get it running.
The basic idea is to install the plotutils library and then you need
to compile the biggles library against that. This compilation is
automatted in the typical
python setup.py build
step but it requires compilation tools, like a C-compiler.
I have honestly no idea how that works on Windows... If you don't
manage to get Biggles running, there is also good plotting methods
included in the SciPy package. SciPy surely comes with ready-made
windows installers. Just that you will then have to create all your
plots from scratch and cannot use the ones that are already built-into
Biskit.
For very quick and dirty plotting, gnuplot is very useful and is used
by some Biskit methods too. So if you just install gnuplot (described
in the windows install section on biskit.fr) you will already be able
to quickly make some simple scatter, line plots and histograms.
That's actually what I am using most of the time.
Hope that helps,
Raik
On Wed, Jan 4, 2012 at 1:09 AM, Asma Tahir <asm...@gm...> wrote:
> Hi Raik,
>
> Thank you so much for your reply!
>
> Yup, I am using Windows. Your recommendations helped me a lot but now I got
> stuck at the end.... (I have added the trunk folder in
> C:\Python27\lib\site-packages\Biskit)
>
> When I type import Biskit in python, it will give me following error
> message:
>
> Warning: Could not import PVM (Parallel Virtual Machine) modules. Please
> check that pvm and pypvm are installed.
> Warning: Could not import biggles module. Plotting is not available.
>
> Biggles and PVM is already in the Trunk folder (The one I put in Biskit
> folder).
>
> For the other two commands (for numpy and Scientific), no error message at
> all.
>
> Please advice.
>
> Thank You and Best Regards,
>
> Asma Ishaq Tahir
> Research Technical Assistant
>
> On Wed, Jan 4, 2012 at 5:44 AM, Raik Gruenberg <rai...@cr...>
> wrote:
>>
>> Hi Asma,
>>
>> you are trying a Windows installation, right? I haven't tested that in
>> a very long time. In any case, the current installation packages on
>> sourceforge are rather out of date. I have started working on a new
>> release but hadn't the time yet to finish it.
>>
>> On Windows, your best bet for the moment is to install things manually:
>> 1) python
>> 2) numpy
>> 3) scientific python
>> As briefly described on
>> http://biskit.pasteur.fr/install/windows_install/ but you should of
>> course use more recent versions of everything.
>>
>> Make sure that numpy and Scientific Python can be used from the python
>> you installed. E.g. open an a python interpreter and enter:
>>
>> import numpy
>> import Scientific
>>
>> Both should run through without error messages.
>>
>> Then use SVN to retrieve the current development snapshot of biskit.
>> There are also some graphical tools. Or you download and unpack the
>> daily source tarball from Sourceforge:
>> http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/?view=tar
>>
>> Unpack the content of this archive file into a folder named
>> 'biskitproject' or similar. And then add the folder
>> C:\....biskitproject/Biskit to your PYTHONPATH.
>>
>> python
>> import Biskit
>>
>> should then work (the first time, you will receive messages about
>> config files that are being created).
>>
>>
>> One note of caution -- Biskit on Windows is rather untested territory.
>> I suspect that many of the third-party software wrappers will probably
>> not work.
>>
>> I hope this is helping somewhat. Please tell me if you get it running.
>> Perhaps you could then help to update the installation section on the
>> web site.
>>
>> Greetings,
>> Raik
>>
>>
>> On Tue, Jan 3, 2012 at 2:26 AM, Asma Tahir <asm...@gm...> wrote:
>> > Greetings!
>> >
>> > I encountered problem in installing biskit. I have already installed
>> > python
>> > 2.5 but numpy is unable to found the python 2.5 in registry. I also have
>> > python 2.7. Biskit.exe can recognize only python 2.7 but not python 2.5.
>> >
>> > Kindly advice.
>> >
>> > Thank you and Best Regards,
>> >
>> >
>> > *Asma Ishaq Tahir*
>> > *Research Technical Assistant*
>> >
>> > ------------------------------------------------------------------------------
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>>
>>
>>
>> --
>> --
>> ___________________________________
>> Raik Grünberg
>> http://www.raiks.de/contact.html
>> ___________________________________
>
>
--
--
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
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