I've installed Galaxy in local and following the Tool dependencies manual I installed all necessary tools. However for some of then such as BWA, Bowtie,... it's usually needed to create indexes.

Where should I store those indexes? In the galaxy directory or in each tool directory? How can I tell galaxy where the indexes are?

I find a manual's page talking about it /http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup), suggesting to organize the various index files for each build, but I don't know if these folders should be stored into Galaxy directory (eg. in tool-data directory) or what.

Could you please explain this a little?

Thank you and regards,