I've just upgraded a galaxy instance from the Nov 2013 release to the current. I had a few issues, mostly related to tool migration.
1) The entires in the tool_conf.xml file were not deleted as they should have been. This is a pain, but I can fix it (though it will take some time)
2) The repo directories in tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ were never created (e.g. there was no bowtie2 directory there). I did uninstall and reinstall bowtie2 as a test, and the tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2 directory was created. However, it seems that Galaxy now looks for the bowtie2 indicies in tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/96d2e31a3938/bowtie2_indicies.loc instead of in tool-data/bowtie2_indicies.loc. How should I maintain these indicies going forward? Do I need to manually update the tool_data_table_conf.xml for each migrated tool?
Thanks for any help or suggestions.