install.mac4.txt

NECESSARY STEPS FOR TURNING YOUR MAC INTO A SCIENTIFIC COMPUTING PLATFORM  Last updated April 2012

Instructions for updating a Mac from Leopard to Snow Leopard can be found at http://artsci.wustl.edu/~jgill/snowleopard.txt

Prerequisites, install these first

[ ] Apple Developer Connection Xcode (necessary collection of software tools.  Also available on your installation DVD.)
    http://developer.apple.com/tools/download/ 

[ ] X11 for Mac Os X (also available on your installation DVD)
    http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113.html

[ ] A System for installing and managing unix tools like

    - Homebrew 
      http://mxcl.github.com/homebrew/

    - Fink Unix utilities
      http://www.finkproject.org/
      Fink Commander 
      http://finkcommander.sourceforge.net/                                  

Then proceed with everything else as needed.

[ ] MacTeX
    http://tug.org/mactex/
    (Very large, but comprehensive.)

[ ] A Nice LaTeX Editor/Viewer
    - TeXshop for LaTeX 
      http://www.uoregon.edu/~koch/texshop/obtaining.html

[ ] More general editors:
    VI: http://code.google.com/p/macvim/ 
        Pathogen is a great way to manage plugins for vim like Vim-R-Plugin or Vim-LaTeX
        (https://github.com/tpope/vim-pathogen)
    Aquamacs: http://aquamacs.org/
    GNU Emacs: Less Mac-specific modificiations than Aquamacs, but easier to customize across platforms 
 	http://emacsformacosx.com/

[ ] R
    http://cran.wustl.edu/sources.html
    (for binaries http://cran.wustl.edu/)
    (or for development versions and tools to allow building of packages http://r.research.att.com/)

[ ] R standalone math libraries
    "The library is not built automatically when R is installed, but can be built 
    in the directory src/nmath/standalone in the R sources: see the file README there."
    in /Users/jgill/Documents/R-2.4.1/src/nmath/standalone, type "make install"
 
[ ] A Nice R Graphical User Interface 

    - RStudio 
      http://rstudio.org

[ ] JAGS
    http://calvin.iarc.fr/~martyn/software/jags/
    
[ ] VLC
    http://www.videolan.org/vlc/

[ ] freestanding TCL/TK.  Needed by Rcmdr and other programs   
    http://cran.wustl.edu/bin/macosx/tools/

[ ] Open Office
    http://download.openoffice.org/

[ ] Adobe Reader
    http://www.adobe.com/products/acrobat/readstep2.html

[ ] Browsers
    Omniweb: http://www.omnigroup.com/applications/omniweb/
    Firefox: http://www.mozilla.com/en-US/firefox/
    Camino: http://www.caminobrowser.org/
    Google Chrome: http://www.google.com/chrome

[ ] Firefox Extensions
    LibX Washington University: http://library.wustl.edu/research/toolbar/
    Zotero:  http://www.zotero.org/

[ ] PDFtoKeynote
    http://www.cs.hmc.edu/~oneill/freesoftware/pdftokeynote.html

[ ] Text to html
    http://sourceforge.net/project/showfiles.php?group_id=36483&package_id=28791&release_id=261701

[ ] File Transfer Clients
    CyberDuck, http://cyberduck.ch/
    Filezilla, http://filezilla-project.org/

[ ] To Add Nice Equations and Tables to Keynote Presentations
    http://www.apple.com/downloads/macosx/math_science/latexit.html

[ ] Miscellaneous General Advice Sites:
    http://www.apple.com/downloads/macosx/math_science/
    http://hitoshi.berkeley.edu/macosx/
    http://www.macresearch.org/

[ ] For Nice Mac Fonts in LaTeX (XeTeX)
    http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=xetex
    (install with fink install xetex)

[ ] Some Additional Tools:
    BibDesk, http://bibdesk.sourceforge.net/                                                
    Desktop Manager, http://desktopmanager.berlios.de/
    Gimp, http://www.gimp.org/
    Quicksilver, http://en.wikipedia.org/wiki/Quicksilver_(software)                                                                                     
    Combine PDFs, http://www.monkeybreadsoftware.de/Freeware/CombinePDFs.shtml
    Poisoned, http://gottsilla.net/about.php
    Kompozer, http://kompozer.net/