# Most dependancies satisfied by package manager:
$ sudo apt-get install git ipython python-numpy python-scipy \
  python-matplotlib python-scipy python-ply python-cheetah \
  python-reportlab python-sphinx make libncurses5-dev \
  libreadline-dev python-setuptools python-mako python-lxml \
  python-networkx python-pydot

# Lets install all packages locally, to ~/.local/
$ mkdir -p /home/mh/.local/lib/python2.7/site-packages/
$ echo export PYTHONPATH="$PYTHONPATH:~/.local/lib/python2.7/site-packages/" >> ~/.bashrc
$ echo export PATH="$PATH:~/.local/bin" >> ~/.bashrc
$ source ~/.bashrc

# Install neurounits, (which will automatically install 'quantities')
$ easy_install --prefix=~/.local/ neurounits==0.1.2
$ ipython -c 'import neurounits'
$ # <No output displayed means everything is OK>

# It might be best to install django (mreorg dependancy)
# through the package manager:
$ sudo apt-get install texlive-full python-django python-django-dajax

# Install mreorg and mredoc using easy install
$ easy_install --prefix=~/.local/ mreorg==0.1.1 mredoc==0.1

# Test out mreorg:
$ ipython -c 'import mreorg'
$ #< Should throw an error - mreorg expects an environmental variable to be set: >
$ export MREORG_CONFIG=''; ipython -c 'import mreorg'
$ # <No output displayed means everything is OK>

# Test out mredoc by creating a simple doc:
$ ipython
>>> import mredoc
>>> doc = mredoc.Section('Test Document',mredoc.Section('Equations', r"""$x=\frac{-b\pm\sqrt{b^2-4ac}}{2a}$""" ))
>>> doc.to_html("~/mredoc_test_out/")
>>> doc.to_pdf("~/mredoc_test.pdf")
>>> quit
$ chromium-browser ~/mredoc_test_out/index.html
$ evince ~/mredoc_test.pdf

# Install NEURON with Python bindings (thanks to Eilif Muller)
# Download from here: http://neuralensemble.org/people/eilifmuller/
# Install the deb package.
$ ipython -c 'import neuron'
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html
$ #<If you see the above banner, everything is good!>

# And lets add the binaries to the PATH. ARCH is your architecture,
# (probably 'x86_64' or 'i686')
$ echo export PATH="$PATH:/opt/nrn/ARCH/bin" >> ~/.bashrc
$ source ~/.bashrc

# Check all NEURON dependancies satisfied for building mod files:
$ mkdir ~/mf_jnk
$ cd ~/mf_jnk
$ cp /opt/nrn/share/nrn/examples/nrniv/netcon/ampa.mod .

$ nrnivmodl
<.... lots of output...>
Successfully created x86_64/special
$ #<Great, NEURON can build .modfiles!>