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mac_installation.md

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Mac installation

Dependencies

Home Brew

If you don't have home brew installed, install it using:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

For more information look at the homebrew page

It is possible that it will give you warning about not having xcode, in this case you should install xcode from the apple app store and open it to accept the license.

It is also a good idea to put the homebrew path (by default /usr/local/bin ) at the start of your path so that homebrew tools take precedence over osx. This can be done by

export PATH=/usr/local/bin:$PATH

Add this line to your .bash_profile file so that it is executed automatically when starting the shell.

Python

It is recomended to use the python version from homebrew, this can be installed by doing

brew install python

Homebrew Python packages

The following python packages should also be installed from homebrew

  • Numpy
  • SciPy
  • Matplotlib
  • PyQt

This packages can be found in homebrew-python, and they can be installed by doing

brew tap Homebrew/python
brew install numpy
brew install scipy
brew install matplotlib
brew install pyqt

R

R can also be installed from homebrew, it is located in homebre-science. The commands are

brew tap homebrew/science
brew install r

After installing r, some additional r libraries should be installed, this can be done by opening R

r

and then typing

install.packages("arm")
install.packages("car")
install.packages("randomForest")
quit()

VTK

vtk can also be installed from homebrew-science. This should be done after installing PyQt. The command is

brew tap homebrew/science
brew install vtk --with-qt

Mercurial

Mercurial is the version control software used by braviz, and the easyest way to be up to date

 brew install mercurial

Additional python packages

All this packages can be installed through pip, the basic syntax is

pip install <package_name>

The following is the list of required packages

  • nibabel
  • colorbrewer
  • rdflib
  • httplib2
  • psutil
  • pandas
  • mpltools
  • seaborn
  • rpy2
  • tornado
  • futures
  • savReaderWriter
  • xlrd
  • XlsxWriter
  • pyzmq

You can install all of these by typing

pip install --allow-external savReaderWriter nibabel colorbrewer rdflib httplib2 psutil pandas mpltools seaborn rpy2 tornado futures savReaderWriter xlrd XlsxWriter pyzmq

Get braviz

Go to the directory where you would like braviz files downloaded and do

hg clone https://bitbucket.org/dieg0020/braviz

You should now add the braviz directory containing the file setup.py to your PYTHONPATH environment variable

export PYTHONPATH = $PYTHONPATH:<braviz_dict>

You can add that line to your .bash_profile file in order to have braviz always available when you start a terminal

Configuring

The braviz/applications directory contains several configuration files. First there should be a braviz.cfg file, if it doesn't exist it will be automatically created when you first run the system. The second one is a file named <project>_hosts.cfg where <project> is the name of the project you will use (for example kmc400); this file contains the locations of the project files for different computers. Be sure your computer is there with the correct paths. For more information see braviz configuration and host configuration

Run braviz

After meeting all the requirements, and having the code, you should be able to run braviz by doing

python -m braviz.application.braviz_menu2

the first time you launch the system you may require multiple attempts.