getting afni working on mac osx 10.9 mavericks with home-brew

gistfile1.txt

Getting afni working on Mac OSX 10.9 Mavericks, using Homebrew

Briefly: parts of afni (e.g. uber_subject.py) require the pyqt library ... and pyqt requires qt ... but the homebrew install of qt is currently broken on osx mavericks 10.9 ... but there is a patch ... but pyqt also requires sip ... and there is a problem where pyqt doesn't like the version of sip, in particular with a newer haswell CPU macbook pro ... but there is a fix ... and we need to add lines to our .bash_profile for afni ... and be careful if you have other python things installed since afni expects to find python things in certain locations

Here is a step-by-step:

1.	install Xcode command line tools
	
	xcode-select --install

2.	install homebrew
	
	ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"

3.	install Qt4 using Cliff Rowley's patch (https://github.com/mxcl/homebrew/pull/23793)
	* note this could take a while, and your CPU fans will go nuts
	
	brew install https://raw.github.com/cliffrowley/homebrew/patched_qt/Library/Formula/qt.rb --HEAD

4.	install sip

	brew install sip

5.	before installing pyqt, bypass the stdlib dependency tracking, see 2 links below for details
	(this may only apply to you if you have a newer macbook pro with a haswell cpu)
   		https://github.com/mxcl/homebrew/issues/23687#issuecomment-27339429
   		https://github.com/mxcl/homebrew/blob/master/Library/Homebrew/build.rb#L174
	
	- comment out line 174 in /usr/local/Library/Homebrew/build.rb:
	#  stdlib_in_use = CxxStdlib.new(stdlibs.first, ENV.compiler)

6.	install pyqt

	brew install pyqt

7.	un-comment line 174 in /usr/local/Library/Homebrew/build.rb:
	
	stdlib_in_use = CxxStdlib.new(stdlibs.first, ENV.compiler)

8.	install wget so we can download stuff from the interwebs using the command line

	brew install wget

9. download and install XQuartz (to provide X11)

	wget http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.4.dmg -P ~/Downloads/
	open ~/Downloads/XQuartz-2.7.4.dmg
	open /Volumes/XQuartz-2.7.4/XQuartz.pkg

	and follow the GUI instructions for install
	then unmount and delete the installer

	umount /Volumes/XQuartz-2.7.4/
	rm -fr ~/Downloads/XQuartz-2.7.4.dmg

9.	download afni to your ~/Downloads folder

	wget http://afni.nimh.nih.gov/pub/dist/tgz/macosx_10.7_Intel_64.tgz -P ~/Downloads/

10.	install afni to your home directory

	cd ~/Downloads
	tar -xvzf macosx_10.7_Intel_64.tgz
	mkdir ~/afni
	cp -r ~/Downloads/macosx_10.7_Intel_64/* ~/afni/
	/bin/rm -fr ~/Downloads/macosx_10.7_Intel_64*

11.	add some stuff to your .bash_profile file:

	export PATH=~/afni:$PATH
	export DYLD_FALLBACK_LIBRARY_PATH=~/afni
	export PYTHONPATH=/usr/local/lib/python2.7/site-packages

	* note that if you have other python stuff installed,
	* e.g. the Enthought or Anaconda python distributions,
	* then you probably have lines like this in your .bash_profile:
	* that you will have to comment out (and re-start bash)
	* before using afni:
	* 		export PATH="/Users/plg/anaconda/bin:$PATH"

12.	open up a new terminal and run afni or uber_subject.py

	afni
	uber_subject.py