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