Neuron with Python on Ubuntu 11.10 32 bit

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lneisenman
Posts: 20
Joined: Wed Dec 16, 2009 10:26 am

Neuron with Python on Ubuntu 11.10 32 bit

Post by lneisenman » Wed Nov 16, 2011 10:18 am

I had to set up Neuron on a new install of 32 bit Ubuntu 11.10 running in Virtualbox. Based on some recent posts about dependencies (viewtopic.php?f=6&t=2387#p9420 and viewtopic.php?f=6&t=1772#p9596) and some trial and error, I came up with the following script. It obviously includes some extras that can be omitted but the first two sections seem to provide all the requirements to build Neuron. Make the file, which I called setup.sh, executable (right click on the file, choose properties, choose the permissions tab and click the "Allow executing file as program" box). Double clicking on the file brings up a dialog with several choices. Choose "Run in Terminal" and everything should get installed.

For future reference, is there a better way to do this?

Code: Select all

#Basics to compile neuron with python
sudo apt-get install build-essential
sudo apt-get install libxext-dev
sudo apt-get install libncurses-dev
sudo apt-get install python-dev
sudo apt-get install xfonts-100dpi
#If this produces a funny looking EULA with <OK> at the bottom
#Hit the tab key and then the enter key to proceed

#Here is my config command
#./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv-17 --with-nrnpython --with-numpy

#Mercurial and tools to build from repository
sudo apt-get install mercurial
sudo apt-get install bison
sudo apt-get install flex
sudo apt-get install automake
sudo apt-get install libtool

#Lapack and fortran for building Numpy/Scipy
#Building the current versions is easy enough that I don't bother with the older packages
sudo apt-get install liblapack-dev
sudo apt-get install gfortran

#Python setup
sudo apt-get install python-setuptools
sudo apt-get install python-matplotlib	# this also installs an older version of numpy
sudo easy_install -U ipython

#Spyder IDE setup
sudo apt-get install libqt4-dev
sudo apt-get install pyqt4-dev-tools
sudo apt-get install tortoisehg
sudo easy_install -U Sphinx
sudo easy_install -U rope
sudo easy_install -U pyflakes
sudo easy_install -U pep8
sudo easy_install -U spyder

hines
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Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Neuron with Python on Ubuntu 11.10 32 bit

Post by hines » Thu Nov 17, 2011 3:50 pm

That seems complete to me. I have installed numpy and scipy using the Ubuntu Software center without
directly asking for gfortran or lapack.

I am in the process of preparing a 7.2 standard distribution and was experimenting with building the rpm and
deb file under ubuntu11.10. I was pleasantly surprised that I could install on a bare ubuntu11.10 from
http://www.neuron.yale.edu/ftp/neuron/versions/alpha
by clicking on the nrn-7.2.alpha-549.i686.deb file and accepting the "open with" of Ubuntu Software Center.
One still needs to apt-get xfonts-100dp to avoid the "unable to open font" notice
and also python-dev
to be able to embed python (Otherwise, I guess, the shared libraries are missing).
Unfortunately, I don't know how robust the deb file is for other ubuntu or debian systems.

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