##OSX Setup (From Scratch - Mavericks)

###Index

1. Add Home Directory to the SideBar of Finder
2. Install and Setup Divvy
3. Install and activate Hyperdock
4. Install XCode Command Line tool

1. Add Home Directory to the SideBar of Finder

   • Press CMD+SHIFT+H to enter your Home folder in Finder
   • Press CMD+ArrowUp to get into the Users folder
   • Drag the folder of your choice to the Sidebar

2. Install and Setup Divvy

   • Download Divvy from http://mizage.com/divvy/

   • Click the Divvy icon shown on the upper right of your screen

     

   • Click the cogwheel icon and then click License. Enter the following details:

     Name:	JeffreyTang
     Code:	GAXAE-F9AXC-M5EAU-UFRKM-RPMMA-NYR9E-8ZPZ9-64JH9-A9KQB-VNRHM-DU6W6-T4Y68-XEPCL-UH76Y-V7B82-H4 
     

3. Install and activate Hyperdock

   • Download HyperDock from http://hyperdock.bahoom.com/
   • Activate by double clicking jeffrey.tang09@gmail.com.hdlicense in Finder

4. Dock Settings

   

5. Install XCode Command Line tool

   xcode-select --install

6. Install and Setup iTerm as Guake

   • See iterm_setup.md

7. Install gfortran

   • Download relevant dmg from https://gcc.gnu.org/wiki/GFortranBinaries#MacOS

8. Install XQuartz

   • Download the relevant dmg from http://xquartz.macosforge.org/landing/

9. Download PostGres App

   • Go to http://postgresapp.com/
   • Click Download
   • Double click Postgres.app
   • Add /Applications/Postgres.app/Contents/Versions/9.4/bin to your $PATH

10. Install brew

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

11. Packages to install with brew

brew install wget
brew install Caskroom/cask/java
brew install maven
brew install tmux
brew install cowsay
brew install postgis
brew install osm2pgsql
brew install graphviz
brew install cmake # For OpenCV
brew install ffmpeg # For OpenCV
brew link --overwrite gcc
brew tap homebrew/science
brew install r
brew install mongodb
ln -sfv /usr/local/opt/mongodb/*.plist ~/Library/LaunchAgents # Start mongo server on start up
launchctl load ~/Library/LaunchAgents/homebrew.mxcl.mongodb.plist # Launch mongo server now
brew install youtube-dl

11. Install zsh

    • wget https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh -O - | sh
    • Restart Shell to activate zshell

12. Install pip

    • sudo easy_install pip

13. Pip installs

    sudo pip install -r requirements.txt
    sudo easy_install --upgrade numpy
    sudo pip install pandas
    sudo rm -rf /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy
    sudo pip uninstall scipy
    sudo pip install scipy # Should be the lastest scipy
    sudo pip install scikit-image
    sudo pip install scikit-learn
    sudo pip install setuptools --upgrade # have to upgrade setuptools before gensim install
    sudo pip install gensim
    pip install PIL  --allow-unverified PIL --allow-all-external # For wordcloud

14. Install Lasagne and Nolearn

    cd ~
    git clone https://github.com/Lasagne/Lasagne.git
    cd Lasagne
    pip install -r requirements.txt
    sudo python setup.py install
    sudo pip install -U -r https://raw.githubusercontent.com/dnouri/kfkd-tutorial/master/requirements.txt
    # Don't delete Lasagne at ~

15. Install statsmodels 0.7dev

    git clone https://github.com/statsmodels/statsmodels.git
    cd statsmodels
    python setup.py build_ext --inplace
    sudo python setup.py install

16. Download opencv

    wget https://github.com/Itseez/opencv/archive/3.0.0.zip
    unzip 3.0.0.zip
    cd opencv-3.0.0
    git clone https://github.com/Itseez/opencv_contrib.git
    mkdir build
    cmake -G "Unix Makefiles"
    make -j8
    sudo make install

17. Download NLTK data

    import nltk
    nltk.download('all')

18. Install boilerpipe

    cd ~
    git clone https://github.com/originell/jpype.git
    cd jpype
    sudo python setup.py install
    sudo pip install bolierpipe

19. Install PySpark

    cd ~
    wget http://d3kbcqa49mib13.cloudfront.net/spark-1.3.1-bin-hadoop1.tgz
    tar -xzvf spark-1.3.1-bin-hadoop1.tgz    
    
    # Add the following lines to ~/.zshrc
    export SPARK_HOME=/Users/jeffreytang/spark-1.3.1-bin-hadoop1
    export PYTHONPATH=$PYTHONPATH:/Users/jeffreytang/spark-1.3.1-bin-hadoop1/python/

20. Install PyCharm / IntelliJ

    • Log in https://account.jetbrains.com/login
    • Download professional versions PyCharm / IntelliJ
    • Pycharm
      • Preferences -> Editor -> General -> Change font size (Zoom) with Ctrl+MouseWheel is enabled
      • Preferences -> Editor -> General -> Appearance -> Show line numbers
      • Preferences -> Editor -> Color & Font -> Theme
      • Preferences -> Appearance & Behavior -> Appearance -> Theme

21. Install Cassandra

    wget http://psg.mtu.edu/pub/apache/cassandra/2.1.5/apache-cassandra-2.1.5-bin.tar.gz
    tar -xzf apache-cassandra-2.1.5-bin.tar.gz
    cd apache-cassandra-2.1.5/bin
    sudo ./cassandra
    ./cqlsh

22. Install igraph

    brew install igraph
    sudo pip install python-igraph

23. Install graph-tool

    • brew install graph-tool #Takes 30 mins to an hour
    • mkdir -p /Users/jeffreytang/Library/Python/2.7/lib/python/site-packages
    • echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> /Users/jeffreytang/Library/Python/2.7/lib/python/site-packages/homebrew.pth

24. Install pyqt (for ete2 plotting)

    brew install sip
    brew install pyqt

    # Testing if pyqt4 is installed properly
    from ete2 import Tree
    t = Tree( "((a,b),c);" )
    t.show()