Hi Dannon, Thanks for the fast reply On 5 February 2013 14:49, Dannon Baker <dannonbaker@me.com> wrote:

Hi Eric,

The threading.Thread issue indicated below has been fixed (the changeset is

already available in galaxy-dist) and isn't eclipse-centric.

Ok somehow I didn't get this update from https://bitbucket.org/galaxy/galaxy-dist even today.

From eclipse, how are you launching galaxy?

I installed a Mercurial plugin in Eclipse, checked out from ' https://bitbucket.org/galaxy/galaxy-dist" ran ./run.sh one time to download the Eggs necessary, installed the eggs in my eclipse PYTHONPATH and put paster.py serve universe_wsgi.ini in a run configuration. The running of galaxy works nicely, my logs are handled by Eclipse and breakpointing works. So I was quite happy with everything, until I asked PyDev for a Code analysis. It turns out that PyDev did not understand the Bunch() classes like "model.Job.states.QUEUED", but also functions in classes that don't have self as a variable or udefined variables that are called. Probably in real life this is not a big problem, because galaxy is running quite flawlessly, so maybe I just misconfigured PyDev. Because of this I was curious if more people tried the "Eclipse way" or maybe another IDE with debugging enabled. Because I think an IDE can be a great advantage over text-editor developing.

Personally for debugging I've found it easier to use the debugging middleware for anything that happens inside a web transaction (sometimes intentionally raising an exception just to kick out to it), and a simple addition of 'import pdb; pdb.set_trace()' for creating breakpoints that I can work through via pdb in the terminal.

Yeah maybe it's better just to debug this way but it feels a bit low tech with all the nice PyDev features in Eclipse. Thanks again, Eric

-Dannon

On Feb 5, 2013, at 5:29 AM, Eric Kuyt <eric.kuijt@wur.nl> wrote:

...

Hi All,

I am Running my local galaxy instance in Eclipse - pydev to make debugging somewhat easier, but now I run into loads of Code errors. It seems that pydev doesn't understand the Bunch() Class frequently used in Galaxy.

But also code errors that maybe could be fixed. such as:

lib/galaxy/jobs/runner/lwr.py:232

#worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), # target=self.run_next ) --> #worker = threading.Thread( name="LwrJobRunner.thread-%d" % i , #target=self.run_next )

Are these real errors or am I doing something wrong.

Is there anyone with more experience in running Galaxy from within Eclipse?

Thanks,

Eric

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