Make GG link to static download.

Fixes #134
Remove comment from otu picking tutorial about picking against IMG version of GG

Fixes #135
Fix spelling of Greengenes

Fixes #136
Update links for precalc files

Change all links to point to thebeast for download.
Add links for variance files which are needed to predict confidence intervals
with predict_metagenomes.py

Fixes #137
Enable reading of gzipped precalculated file

Allow parallel_predict_traits.py to read gzipped file,
when using the --already_calculated option.

Also, remove the merging of the already calculated file with the new predictions.
Much faster and simpler to just cat resulting files manually afterwards.
Update script test data for metagenome_contributions.py

Change input otu table to a simpler and hopefully gg version independent one.
Update test script data for predict_metagenomes.py
Small changes to handling variance table in predict_metagenomes.py

1) Change assertion so it doesn't fail on ids being in different order (only for them missing)
2) Sort variance and gene table to be in same order in the tables
3) Fix up verbose messages to be a bit clearer

Also, make a few small changes to verbose messages.
Add timeout back to all_tests.py and fix indentation bug
Update usage and test data for normalize_by_copy_number.py
Update metagenome tutorial

Fixes #140
Update download links in install to thebeast.
Merge pull request #141 from mlangill/small_doc_fixes

Small documentation fixes and test code changes