galaxy-dev

Download

galaxy-dev@lists.galaxyproject.org

September 2010

40 participants
62 discussions

pdb prompt under galaxy testing
by WANGYi 01 Sep '10

01 Sep '10

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

2 1

Adding Libraries
by Tanguy Le Carrour 01 Sep '10

01 Sep '10

Hello! I've a running instance of Galaxy that works just fine, thanks to Nate Coraor. I would like to add all the files that our centre produces, which is a lot, to the data library, and I would like to automate it. As I see it, there are 3 options: - add the data directly to the database (dataset, library, library_dataset...), but it "may not be" the best choice... - use the upload1 tool, but I need to first create a dataset (there is a dataset reference in the json configuration file isn't it?) - POST my "multiport/form-data" data to "/library_common/upload_library_dataset", but the library_id and folder_id are not the real ids and I haven't found out, yet, where they are coming from! I could really use a advice on which option is the best. Thank you in advance for your help! Best regards, Tanguy LE CARROUR -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

2 1