Setup for a new install [MAC] (after installing Xcode & command line tools)

install.sh

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# WARNING! 
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# Do you use .bashrc for configuration of your shell?? IF so, do this first:
cat '[[ -s ~/.bashrc ]] && source ~/.bashrc' > ~/.bash_profile

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

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# ACK (grep for programmers) http://beyondgrep.com/
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brew install ack
brew install rename
brew install htop
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# BOOST (C++ library)
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brew install boost

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# UNRAR & 7zip
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brew install unrar
brew install p7zip

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# IMAGE MAGICK
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brew install imagemagick --with-fftw --with-librsvg --with-x11
brew install autotrace  # for image to svg autotrace

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# TEX
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brew install Caskroom/cask/mactex # required for better use of matplotlib
export PATH=$PATH:/usr/texbin # This needs to be added to the .bashrc or .bash_profile
source ~/.bashrc

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# MONGODB
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brew install mongodb

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# GIT (-but it is already in command tools?? -yes... but not everything is there...)
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brew install git

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# PYTHON:
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brew tap homebrew/dupes
brew tap homebrew/python
brew tap homebrew/science
brew install python --with-tcl-tk --enable-threads --with-x11 # labels required for correct Pymol installation

# install virtualenv, nose (unittests & doctests on steroids)
pip install virtualenv
pip install nose

# install numpy and scipy
pip install numpy
pip install scipy
# test the numpy & scipy install
python -c 'import numpy ; numpy.test();'
python -c 'import scipy ; scipy.test();'

# helpful libraries
pip install pathlib
pip install jsonpickle
pip install svgwrite

# matplotlib: generate plots
brew install matplotlib --with-cairo --with-tex # also... required for graph/tools

# install panda, seaborn and pyside
pip install pandas
pip install seaborn
brew install qt
brew linkapps qt
pip install -U PySide
pyside_postinstall.py -install

pip install transforms3d

# graphs (graph metrics, social network analysis, layouting)
pip install networkx
brew install graph-tool # this... takes a while...

# html stuff (parsing)
pip install beautifulsoup4

# mongoDB
pip install pymongo

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# MODELLER
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# There is no way around installing it as a .pkg.. follow the steps @ http://salilab.org/modeller/download_installation.html

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# NODE.JS & BOWER
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# There is no way around installing it as a .pkg. get it @ https://nodejs.org/
# Then..
sudo npm install -g bower

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# PYMOL
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brew install pymol

# To make render faster, get the command line version of the unofficial povray port http://megapov.inetart.net/povrayunofficial_mac/
# And add it to the PATH as 'povray'

# For movies...
# Go to wherever you want to have FREEMOL installed... like..
cd ~/local/bin
svn co svn://bioinformatics.org/svnroot/freemol/trunk freemol-trunk
export FREEMOL=~/local/bin/freemol-trunk/freemol
cd freemol-trunk/src/mpeg_encode
./configure
make
make install

# And add 'export FREEMOL=~/local/bin/freemol-trunk/freemol' to your .bashrc
brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265

brew install asciinema ##
asciinema auth ##
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# DSSP
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brew install dssp

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# zRank & zDock
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# Go to http://zdock.umassmed.edu/software/ 
# Register to get the download links
# zRank is precompiled, get zrank2, zrank1 will not work

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# Reduce
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# Get it from http://kinemage.biochem.duke.edu/software/reduce.php
# Download the executable AND the reduce_wwPDB_het_dict.txt file.
# Set the file to the REDUCE_HET_DICT variable

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# SUBLIME TEXT
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# Download and install the .dmg from http://www.sublimetext.com/3
# Follow the steps in https://packagecontrol.io/installation#Simple to install Package Control
#
# -- Packages
# Anaconda
# BracketHighlighter
# GitGutter
# AdvancedNewFile
# FileHeader