Add functions to download UCLUST and FastTree

These two functions will try to download FastTree (and build it using
gcc) and UCLUST. The resulting executables will be copied to the scripts
directory. This is a similar pattern to what was being done with the
denoiser.

Fixes #1246
Remove dependency on cogent for setup.py

This script is now PIP-installable, at least for the base install.
Add MANIFEST.in & minor modifications to setup.py
Add MANIFEST to .gitignore
Add denoiser files to the exclude
Remove qiime_test_data from setup build

Fixes #1246
Change -lm flag for FastTree
Merge branch 'master' of git://github.com/qiime/qiime into issue_1246
Change name from QIIME->qiime
Update app_available

The standard output and standard error streams are no longer seen on
screen, instead these are now redirected to /dev/null.

Add docstring to the function.
Add changes on versions and functionality

The following was changed:
    - Update versions of matplotlib to be greater than 1.1.0 but less
      than 1.3.1.
    - Update version of BIOM to be 1.3.1 only.
    - Redirect the output of app_available to /dev/null
    - Make the building_stack not executed if egg_info is passed as an
      argument to the script.
Fix wrong if statement
Add call to make clean for the denoiser

This ensures that the denoiser is compiled everytime the script is
executed.
Changes to build denoiser

The denoiser's Makefile was specifying rm *.o for the clean rule; if
this was the case and no *.o files existed, this would error out hence
not executing the subsequent lines.

The setup.py function was copying all the files from the
denoiser/FlowgramAlignment/ folder, this now only copies the *.lhs files
and the Makefile.

Add FlowgramAli_4frame to MANIFEST.in so it's not copied on distribution
and upload time.
Merge branch 'master' of git://github.com/qiime/qiime into issue_1246
Delete all the output from the qiime_test_data dir
Bring back qiime_test_data to setup
Merge branch 'issue_1246_delete_files' into issue_1246
Update metadata of and add note to ChangeLog.md
Merge pull request #1268 from ElDeveloper/issue_1246

Modifications to make QIIME pip installable