Commit de2be7b2 authored by Vermaat's avatar Vermaat
Browse files

Add software installation instructions

parent c0b4363c
Software installation
=====================
The following guide gets you a virtual environment with all the necessary
packages installed.
Linux
-----
We assume Ubuntu (12.04 Quantal Quetzal or later) or Debian Linux (7.0 Wheezy
or later), but if you manage to install everything on a different flavour
that's also fine.
You can [download Ubuntu here](http://www.ubuntu.com/) and either install it
directly on your machine, or run it inside
[VirtualBox](https://www.virtualbox.org/).
Python version >= 2.7.3 and < 3.0 is required. This is installed by default on
Ubuntu and Debian Linux. Note that we use Python 2, *not* Python 3.
We need some system packages to be installed. For the following command, you
need sudo rights:
sudo apt-get install -y \
curl python-qt4 libfreetype6-dev libpng12-dev python-cairo \
python-gtk2 python-gtk2-dev git gfortran
From here on, everything is local for the current user.
Install [virtualenv](http://www.virtualenv.org/) and
[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | exclude_profile=1 $SHELL
source ~/.venvburrito/startup.sh
echo "source ~/.venvburrito/startup.sh" >> ~/.bashrc
Note that because of
[a bug](https://github.com/brainsik/virtualenv-burrito/issues/31) in
Virtualenv Burrito we use `exclude_profile=1` and add the relevant line to
`~/.bashrc` manually.
Automatically link PyGTK/Pycairo/PyQt system packages into our virtual
environments:
curl -s https://gist.github.com/martijnvermaat/6111396/raw/postmkvirtualenv > ~/.virtualenvs/postmkvirtualenv
Create a virtual environment (named `programming-course`, but you could choose
any name here):
mkvirtualenv programming-course
Install IPython (version 1.0):
pip install -e git+https://github.com/ipython/ipython#egg=ipython
# or after its 1.0 release: pip install ipython
Install some of the other package we'll use:
pip install pyzmq tornado jinja2 pygments sphinx markdown nose
pip install numpy
pip install matplotlib
pip install biopython
Define a default matplotlib backend:
mkdir -p ~/.matplotlib
echo "backend : GTKCairo" >> ~/.matplotlib/matplotlibrc
Mac OSX Mountain Lion
---------------------
Install
[Xcode from the App Store](https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12
Xcode from the App Store). Start Xcode and install the device support
(Preferences -> Downloads).
Install Xcode command line tools:
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew doctor
xcodebuild -license # accept license
Add user `bin`, and local Python to your `$PATH`:
echo 'export PATH="~/bin:/usr/local/share/python:/usr/local/bin:$PATH"' > .bash_profile
. .bash_profile
We need some system packages:
brew install python --with-brewed-openssl
brew install gfortran
Install [virtualenv](http://www.virtualenv.org/) and
[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
source .venvburrito/startup.sh
Create a virtual environment (named `programming-course`, but you could choose
any name here):
mkvirtualenv programming-course
Install IPython (version 1.0):
pip install -e git+https://github.com/ipython/ipython#egg=ipython
# or after its 1.0 release: pip install ipython
Install some of the other package we'll use:
pip install pyzmq tornado jinja2 pygments sphinx markdown nose
pip install numpy
pip install matplotlib
pip install biopython
......@@ -12,7 +12,7 @@ for more information.
Software installation
---------------------
Todo (copy from our wiki).
See the instructions in `INSTALL.md`.
Editing the slides
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