Updated text for list description
Seperated shell scripts and functionality

Scripts were split and command line functions were put in the scripts
directory. The functions behind the shells were moved to the american
gut site, and names were changed slightly.
removed yourname definition
Merge pull request #22 from wasade/name_fix

removed yourname definition
Changed main title to PDF in Champagne and Limousines font.

Change other fonts to Helvetica throughout.

Added gray circle for "Missing data" to ball_legend.pdf.

Fixed figure1_ovals.png to right colors.
Removed line defining \yourname
bug fix
ignore contested greengenes taxons that throw off the rare taxon list
Merge pull request #24 from wasade/otu_sig_fix

bug fix
Added line (\hrule) below title and made slight changes to header spacing.
Merge branch 'master' of https://github.com/qiime/American-Gut into module2_modularization

Conflicts:
	scripts/generate_otu_signifigance_tables_AGP.py
Test Code for Make Phyla Plots!
Added unclassified description above the famoly level
methods for fetching unique/rare taxa
Merge pull request #25 from JWDebelius/module2_modularization

Module2 modularization
Removed "Fold" column from second table.
addressing comments
Add VIM swap files and OSX .DS_Store to .gitignore
Merge pull request #27 from ElDeveloper/gitignore_improvements

Add VIM swap files and OSX .DS_Store to .gitignore
Changed paper size to 8.5x13.13636 which is same aspect ratio
as 11x17, the desired print size.  Adjusted float placement
to make them look good in new paper size.