tool_data_table_conf.xml entries for migrated tools

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tool_data_table_conf.xml entries for migrated tools

Lance Parsons
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.

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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