I've installed Galaxy in local and following the Tool
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,

Rafa Hernández de Diego

Genomics of Gene Expression Lab.
Bioinformatics and Genomics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/ Eduardo Primo Yúfera 3
46012 Valencia, Spain
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