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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