Kevin, Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information. (Note that this topic is better suited to galaxy-dev instead of galaxy- user since it's about local installations.) Regards, Kelly Galaxy Team On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:

Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml

May I know if there's a reason for this?

Cheers Kevin _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user