>   1. Is there any help file explaining directory structure and what
>   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
>   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:


It's a bit peculiar to my own situation, but it might give you another

Paul Agapow (
Bioinformatics, Centre for Infections, Health Protection Agency

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