Hi Rafa, The .loc files in 'tool-data' directory link the index files with the actual paths so you need to configure each of the .loc files to match where the index files are placed. With that, you can put the index files anywhere you'd like on the file system (preferably outside Galaxy's home directory). As a reference for a working setup, you can rsync (portion) of the data from GalaxyMain (http://wiki.galaxyproject.org/Admin/Data%20Integration) and see how that's setup. Also, you can fire up a cloud instance and see how it's setup. Hope this helps, Enis On Thu, Feb 21, 2013 at 12:14 AM, Rafael Hernández <rafahd87@gmail.com>wrote:

Hi,

I've installed Galaxy in local and following the Tool dependencies<http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies> 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,

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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