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 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- jt James Taylor Assistant Professor Department of Biology Department of Mathematics & Computer Science Emory University