MOODS dependency not referenced

[ebirn]

MOODS module is used, but no reference in requirements.txt or setup.py/setup.cfg

reg-gen/rgt/motifanalysis/Motif.py

Line 13 in 79d5b2c

from MOODS import tools, parsers

only reference seen in .travis.yml, call to rgt-motifanalysis script fails

login0 [~]> rgt-motifanalysis 
Traceback (most recent call last):
  File "/software/RGT/0.11.7-foss-2018b-Python-2.7.15/bin/rgt-motifanalysis", line 11, in <module>
    load_entry_point('RGT==0.11.7', 'console_scripts', 'rgt-motifanalysis')()
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 476, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2700, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2318, in load
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2324, in resolve
  File "/software/RGT/0.11.7-foss-2018b-Python-2.7.15/lib/python2.7/site-packages/rgt/motifanalysis/Main.py", line 16, in <module>
    import Match
  File "/software/RGT/0.11.7-foss-2018b-Python-2.7.15/lib/python2.7/site-packages/rgt/motifanalysis/Match.py", line 22, in <module>
    from .Motif import Motif, ThresholdTable
  File "/software/RGT/0.11.7-foss-2018b-Python-2.7.15/lib/python2.7/site-packages/rgt/motifanalysis/Motif.py", line 13, in <module>
    from MOODS import tools, parsers
ImportError: No module named MOODS

Best,
Erich

[fabio-t]

This should actually be fixed in setup.py, yes. It's not available on pypi yet (I've asked the author a long time ago), and on our instructions it's stated you should install it if you wish to use motif analysis (which is also what you see in the travis config file):

pip install https://github.com/fabioticconi/MOODS/tarball/pypi-ready

We'll see if we can put a fix in for the next release.

[fabio-t]

Fixed via 71e3f4f