Gaurav

1. Is there any help file explaining directory structure and what all configuration files used for?

The Galaxy wiki is the best place to go for these things, as Louise-Amelie said. You should be able to ignore most things in the config files initially as they will "just work". You can ignore most of the directory structure as well, except perhaps the "tools" directory.

2. I got list of all dependencies from website, Do I have to install all tools in /usr/local/bin/ or can be installed at any custom location?

Mostly, the install should (again) "just work" (install the tarball or distrib and run). I've a got a Galaxy installation checklist here: <http://www.agapow.net/science/bioinformatics/galaxy/installing-galaxy> It's a bit peculiar to my own situation, but it might give you another point-of-view. ---- Paul Agapow (paul-michael.agapow@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************