Hi James,
I don't know if I can offer the whole story on why you're seeing that error, but at first glance it looks like the unit test scripts are assuming that all dependencies are installed for all tools. In particular, the GeneTrack tools.
Here's a practical answer that's probably more helpful anyway:
You are missing dependencies for GeneTrack. When I recently resolved this problem on our local instance, I had to install the following dependencies:
The one your error refers to: PyTables http://www.pytables.org/moin
And its dependencies: numexpr http://code.google.com/p/numexpr/ Cython http://cython.org/ HDF5 (C libraries) http://www.hdfgroup.org/HDF5/
Be sure to read the READMEs and installation notes to be sure you get the right version for your system. It'll take a little bit of time to install all of these (HDF5, especially).
Hope that was helpful. Good luck!
Best, Eric
________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of James Boocock [smilefreak@gmx.com] Sent: Tuesday, December 13, 2011 1:19 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] error when running UNIT_TEST script
Hi When running the run_unit_tests.sh script on my server i get the following Error. Wondering what It means and whether It is something I have done or something within galaxy
#Start Error
Doctest: galaxy.web.form_builder.TextArea ... ok TextField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.TextField ... ok
====================================================================== ERROR: Failure: ImportError (No module named tables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/james/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/home/james/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/james/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/james/galaxy-dist/lib/galaxy/datatypes/converters/bed_to_genetrack_converter.py", line 16, in <module> from genetrack.scripts import tabs2genetrack File "/home/james/galaxy-dist/eggs/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg/genetrack/__init__.py", line 38, in <module> from genetrack.hdflib import PositionalData File "/home/james/galaxy-dist/eggs/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg/genetrack/hdflib.py", line 5, in <module> from tables import openFile ImportError: No module named tables
---------------------------------------------------------------------- Ran 60 tests in 11.380s
#End Error
Cheers James ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: