Commit 28f26e1b authored by Michiel van Galen's avatar Michiel van Galen
Browse files

Updating the curl command

parent 051b5485
Software installation Software installation
===================== =====================
The following guide gets you a virtual environment with all the necessary The following guide gets you a virtual environment with all the necessary
packages installed. packages installed.
Linux Linux
----- -----
We assume Ubuntu (12.04 Quantal Quetzal or later) or Debian Linux (7.0 Wheezy 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 or later), but if you manage to install everything on a different flavour
that's also fine. that's also fine.
You can [download Ubuntu here](http://www.ubuntu.com/) and either install it You can [download Ubuntu here](http://www.ubuntu.com/) and either install it
directly on your machine, or run it inside directly on your machine, or run it inside
[VirtualBox](https://www.virtualbox.org/). [VirtualBox](https://www.virtualbox.org/).
Python version >= 2.7.3 and < 3.0 is required. This is installed by default on 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. 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 We need some system packages to be installed. For the following command, you
need sudo rights: need sudo rights:
sudo apt-get install -y \ sudo apt-get install -y \
curl python-qt4 libfreetype6-dev libpng12-dev python-cairo \ curl python-qt4 libfreetype6-dev libpng12-dev python-cairo \
python-gtk2 python-gtk2-dev git gfortran python-gtk2 python-gtk2-dev git gfortran
From here on, everything is local for the current user. From here on, everything is local for the current user.
Install [virtualenv](http://www.virtualenv.org/) and Install [virtualenv](http://www.virtualenv.org/) and
[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using [virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito): [Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL curl -sL https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
source ~/.venvburrito/startup.sh source ~/.venvburrito/startup.sh
Automatically Automatically
[link PyGTK/Pycairo/PyQt system packages](https://gist.github.com/martijnvermaat/6111396/) [link PyGTK/Pycairo/PyQt system packages](https://gist.github.com/martijnvermaat/6111396/)
into our virtual environments: into our virtual environments:
curl -s https://gist.github.com/martijnvermaat/6111396/raw/postmkvirtualenv > ~/.virtualenvs/postmkvirtualenv curl -sL https://gist.github.com/martijnvermaat/6111396/raw/postmkvirtualenv > ~/.virtualenvs/postmkvirtualenv
Create a virtual environment (named `programming-course`, but you could choose Create a virtual environment (named `programming-course`, but you could choose
any name here): any name here):
mkvirtualenv programming-course mkvirtualenv programming-course
Install IPython: Install IPython:
pip install ipython pip install ipython
Install some of the other package we'll use: Install some of the other package we'll use:
pip install pyzmq tornado jinja2 pygments sphinx markdown nose pip install pyzmq tornado jinja2 pygments sphinx markdown nose
pip install numpy pip install numpy
pip install matplotlib pip install matplotlib
pip install biopython pip install biopython
Define a default matplotlib backend: Define a default matplotlib backend:
mkdir -p ~/.matplotlib mkdir -p ~/.matplotlib
echo "backend : GTKCairo" >> ~/.matplotlib/matplotlibrc echo "backend : GTKCairo" >> ~/.matplotlib/matplotlibrc
Mac OSX Mountain Lion Mac OSX Mountain Lion
--------------------- ---------------------
Install Install
[Xcode from the App Store](https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12 [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 Xcode from the App Store). Start Xcode and install the device support
(Preferences -> Downloads). (Preferences -> Downloads).
Install Xcode command line tools: Install Xcode command line tools:
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)" ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew doctor brew doctor
xcodebuild -license # accept license xcodebuild -license # accept license
Add user `bin`, and local Python to your `$PATH`: Add user `bin`, and local Python to your `$PATH`:
echo 'export PATH="~/bin:/usr/local/share/python:/usr/local/bin:$PATH"' > .bash_profile echo 'export PATH="~/bin:/usr/local/share/python:/usr/local/bin:$PATH"' > .bash_profile
. .bash_profile . .bash_profile
We need some system packages: We need some system packages:
brew install python --with-brewed-openssl brew install python --with-brewed-openssl
brew install gfortran brew install gfortran
Install [virtualenv](http://www.virtualenv.org/) and Install [virtualenv](http://www.virtualenv.org/) and
[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using [virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito): [Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
source .venvburrito/startup.sh source .venvburrito/startup.sh
Create a virtual environment (named `programming-course`, but you could choose Create a virtual environment (named `programming-course`, but you could choose
any name here): any name here):
mkvirtualenv programming-course mkvirtualenv programming-course
Install IPython (version 1.0): Install IPython (version 1.0):
pip install -e git+https://github.com/ipython/ipython#egg=ipython pip install -e git+https://github.com/ipython/ipython#egg=ipython
# or after its 1.0 release: pip install ipython # or after its 1.0 release: pip install ipython
Install some of the other package we'll use: Install some of the other package we'll use:
pip install pyzmq tornado jinja2 pygments sphinx markdown nose pip install pyzmq tornado jinja2 pygments sphinx markdown nose
pip install numpy pip install numpy
pip install matplotlib pip install matplotlib
pip install biopython pip install biopython
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