On Nov 9, 2012, at 12:56 AM, Derrick Lin wrote:
For issue 1), so I think it's safe to remove the tool-data/tool_data_table_conf.xml & tool-data/tool_data_table_conf.xml.sample since they are not used?
Yes, the ~/tool-data/tool_data_table_conf.xml.sample and ~/tool-data/tool_data_table_conf.xml.sample files can be removed.
For issue 2) if the galaxy will automatically pick up the new file shed_tool_data_table_conf.xml without configuring the ini file?
Yes, no changes are necessarey in your universe_wsgi.ini file unless you want to name these particular files differently than these default names. The change set I committed includes entries in universe_wsgi.ini.sample for both of these files (the tool_data_table_conf.xml file was never added to the sample ini), but adding the new settings to the universe_wsgi.ini file is not required as the default names will be used.
Also how does this change affect the existing shed tools like BWA that is using tool_data_table_conf.xml?
The existing shed tools will contiue to function as usual, but entries for them will be in the tool_data_table_conf.xml file. ANy new tools installed from the tool shed that use entries like this will be added to the new shed_tool_data_table_conf.xml file. Entries from both of these files are loaded into the ToolDataTableManager. The intent is for the Galaxy admin to be able to manuall make changes to the tool_data_table_conf.xml file and not have them munged by the tool shed's installation process. This is the same approach used for the tool_conf.xml file, where the Galaxy tool shed repository installation process uses the shed_tool_conf.xml file.
Greg Von Kuster