update install instructions

[ebolyen]

Trying to install this, but I am running into the issue where the project itself requires biom 1.2.0 (not on pypi, and 1.3.1 doesn't seem to work) however the ipython notebooks require biom 2.0.0

[gregcaporaso]

yeah, i need to update that. i believe these are the current deps, but will confirm:

IPython >= 2.0.0
short-read-tax-assignment repo (currently the short-read-tax-assignment/code dir needs to be in your PYTHONPATH, related to #72)
scikit-bio == 0.1.4 (takes care of the pandas and mpl deps)
biom-format >= 2.0.1

[ebolyen]

Tests fail for biom-format 2.0.1:

(shortread)evan@evan-ubuntu:~/biocore/short-read-tax-assignment$ nosetests code
...EE
======================================================================
ERROR: Failure: ImportError (cannot import name DenseTable)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/evan/biocore/short-read-tax-assignment/code/tests/test_generate_taxa_compare_table.py", line 14, in <module>
    from taxcompare.generate_taxa_compare_table import *
  File "/home/evan/biocore/short-read-tax-assignment/code/taxcompare/generate_taxa_compare_table.py", line 14, in <module>
    from qiime.workflow.util import WorkflowError
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/qiime/workflow/util.py", line 20, in <module>
    from qiime.util import (qiime_system_call,
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/qiime/util.py", line 42, in <module>
    from biom.table import DenseTable
ImportError: cannot import name DenseTable

======================================================================
ERROR: Failure: ImportError (cannot import name DenseTable)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/evan/biocore/short-read-tax-assignment/code/tests/test_multiple_assign_taxonomy.py", line 21, in <module>
    from qiime.test import initiate_timeout, disable_timeout
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/qiime/test.py", line 24, in <module>
    from qiime.util import qiime_system_call, get_qiime_temp_dir
  File "/home/evan/.virtualenvs/shortread/local/lib/python2.7/site-packages/qiime/util.py", line 42, in <module>
    from biom.table import DenseTable
ImportError: cannot import name DenseTable

[ebolyen]

I pip installed the exact commit referenced for qiime.

[gregcaporaso]

don't worry about the tests for now, a lot of the code is being gutted. just worry about having the 1-evaluation-framework notebook (which is the one I linked you to earlier) working. Sorry for the confusion.