Remove test for unused function parse_marker_gene_copy_numbers

Addresses #8
Remove test_make_test_trees.py

Addresses #6 and #13
Testing is now done in test_make_test_datasets.py
Remove scripts/format.py

Addresses #21
Change scripts and tests to be executable

A few scripts and tests were did not have executable permissions.
Remove unneeded print statements (to stdout)

Remove stdout from test_evaluate_test_datasets.py and evaluate_test_datasets.py
Remove stdout messages from make_test_datasets.py and its test script.
Opted to remove print statements instead of commenting
Remove test for unused function parse_marker_gene_copy_numbers

Addresses #8
Remove test_make_test_trees.py

Addresses #6 and #13
Testing is now done in test_make_test_datasets.py
Remove scripts/format.py

Addresses #21
Change scripts and tests to be executable

A few scripts and tests were did not have executable permissions.
Remove unneeded print statements (to stdout)

Remove stdout from test_evaluate_test_datasets.py and evaluate_test_datasets.py
Opted to remove print statements instead of commenting
Merge branch 'remove_unneeded_tests' of github.com:mlangill/picrust into remove_unneeded_tests

Conflicts:
	picrust/make_test_datasets.py
Merge pull request #28 from mlangill/remove_unneeded_tests

Remove unneeded tests
modified ace.py to raise error on when R prints to stderr

I think in general that if R is reporting an issue in stderr, we want PICRUSt to fail. Is this not accurate? It definitely plays nicer with ``all_tests.py`` - see below. If the ace R code sometimes reports things like progress reports on stderr, then we don't want to merge this change.

**Before this change** it's not really possible to tell what's going on with the test failure:

```
python tests/all_tests.py
EEEE................................................................
======================================================================
ERROR: test_ace_for_picrust_ml (test_ace.AceTests)
test_ace_for_picrust with method 'ML' functions as expected with valid input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 66, in test_ace_for_picrust_ml
    actual,actual_ci= ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="ML")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 63, in ace_for_picrust
    print "R wrote this to stderr:"
  File "tests/all_tests.py", line 54, in write
    raise RuntimeError, "Output not allowed in tests"
RuntimeError: Output not allowed in tests

======================================================================
ERROR: test_ace_for_picrust_pic (test_ace.AceTests)
test_ace_for_picrust with method 'pic' functions as expected with valid input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 84, in test_ace_for_picrust_pic
    actual,actual_ci= ace_for_picrust(self.in_tree1_fp,self.in_trait1_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 63, in ace_for_picrust
    print "R wrote this to stderr:"
  File "tests/all_tests.py", line 54, in write
    raise RuntimeError, "Output not allowed in tests"
RuntimeError: Output not allowed in tests

======================================================================
ERROR: test_ace_for_picrust_pic_single_trait (test_ace.AceTests)
test_ace_for_picrust with method 'pic' functions as expected with single column trait table
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 99, in test_ace_for_picrust_pic_single_trait
    actual,ci= ace_for_picrust(self.in_tree1_fp,self.in_trait2_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 63, in ace_for_picrust
    print "R wrote this to stderr:"
  File "tests/all_tests.py", line 54, in write
    raise RuntimeError, "Output not allowed in tests"
RuntimeError: Output not allowed in tests

======================================================================
ERROR: test_ace_for_picrust_pic_with_funky_tip_labels (test_ace.AceTests)
test_ace_for_picrust for a tree with underscores in tip labels
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 106, in test_ace_for_picrust_pic_with_funky_tip_labels
    actual,ci= ace_for_picrust(self.in_tree2_fp,self.in_trait3_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 63, in ace_for_picrust
    print "R wrote this to stderr:"
  File "tests/all_tests.py", line 54, in write
    raise RuntimeError, "Output not allowed in tests"
RuntimeError: Output not allowed in tests

----------------------------------------------------------------------
Ran 68 tests in 2.189s

FAILED (errors=4)
R wrote this to stderr:R wrote this to stderr:R wrote this to stderr:R wrote this to stderr:
```

**After this change** the test failures are more informative:

```
python tests/all_tests.py
EEEE................................................................
======================================================================
ERROR: test_ace_for_picrust_ml (test_ace.AceTests)
test_ace_for_picrust with method 'ML' functions as expected with valid input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 66, in test_ace_for_picrust_ml
    actual,actual_ci= ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="ML")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 65, in ace_for_picrust
    " %s" % "\n".join(result["StdErr"].readlines()))
RuntimeError: R reported an error on stderr: sh: /Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/support_files/R/ace.R: Permission denied

======================================================================
ERROR: test_ace_for_picrust_pic (test_ace.AceTests)
test_ace_for_picrust with method 'pic' functions as expected with valid input
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 84, in test_ace_for_picrust_pic
    actual,actual_ci= ace_for_picrust(self.in_tree1_fp,self.in_trait1_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 65, in ace_for_picrust
    " %s" % "\n".join(result["StdErr"].readlines()))
RuntimeError: R reported an error on stderr: sh: /Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/support_files/R/ace.R: Permission denied

======================================================================
ERROR: test_ace_for_picrust_pic_single_trait (test_ace.AceTests)
test_ace_for_picrust with method 'pic' functions as expected with single column trait table
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 99, in test_ace_for_picrust_pic_single_trait
    actual,ci= ace_for_picrust(self.in_tree1_fp,self.in_trait2_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 65, in ace_for_picrust
    " %s" % "\n".join(result["StdErr"].readlines()))
RuntimeError: R reported an error on stderr: sh: /Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/support_files/R/ace.R: Permission denied

======================================================================
ERROR: test_ace_for_picrust_pic_with_funky_tip_labels (test_ace.AceTests)
test_ace_for_picrust for a tree with underscores in tip labels
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/caporaso/Dropbox/code/picrust/tests/test_ace.py", line 106, in test_ace_for_picrust_pic_with_funky_tip_labels
    actual,ci= ace_for_picrust(self.in_tree2_fp,self.in_trait3_fp, method="pic")
  File "/Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/ace.py", line 65, in ace_for_picrust
    " %s" % "\n".join(result["StdErr"].readlines()))
RuntimeError: R reported an error on stderr: sh: /Users/caporaso/.virtualenvs/picrust/lib/python2.7/site-packages/picrust/support_files/R/ace.R: Permission denied

----------------------------------------------------------------------
Ran 68 tests in 2.191s

FAILED (errors=4)
```
modified call to ace.R so the call is actually to R

this gets around the package data permissions issue, which is tricky and ugly with DistUtils
added more detailed comment
Merge pull request #44 from gregcaporaso/issue-43

Issue 43