Are you trying to use PDB to debug your tools or Galaxy itself? I'm assuming the
former. If that is the case, you are likely to encounter a lot of problems. If you run
Galaxy under PDB, it will not debug your tool since that is a separate child process. If
you add pdb to the tool config, you will have difficulty communicating with it since
Galaxy is handling stdin and stdout.
The best approach is likely to take the command line used to invoke your tool from the
log, and run it directly in PDB, taking Galaxy out of the equation entirely.
On Sep 1, 2010, at 2:19 AM, WANGYi wrote:
Hi Galaxy dev team,
This is Yi WANG, developer from a team aiming to integrate some own tools into Galaxy
framework for the tools' web application.
We have finished the tool configs and are currently testing our tools under Galaxy
testing framework. Sometimes when there are some exceptions raised during the tests, we
would like to debug into our tool codes to see what had happed in detail. And we use
python debug 'pdb' for this purpose.
But when a breakpoint is reached during the test, we expect but are not able to see any
pdb prompt (debug interface) or debug information from the console (although we are sure
that the testing does pause for the break point), which makes the debug procedure rather
difficult.
And still, it is weird that, after we type "quit" command to exit pdb (the
testing will of course resume), the log of the testing will then display the debug
information which should have appeared previously under 'pdb' prompt.
Could you please give us some hints on this? Any advice on this issue will be really
appreciated. Thanks so much.
Regards
Yi WANG
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-- jt
James Taylor
Assistant Professor
Department of Biology
Department of Mathematics & Computer Science
Emory University