I think we need like 10 pages of manual to install galaxy on local machines. The main problem I have is limited space on usegalaxy and inability to install an appropriate copy on the university server. i and many others have the same problems over and over again. I think somebody need to address this issue or galaxy will remain the limited platform instead of the one platform. The main problems I guess that we need to address in this manual are:
Install and run on local machine and on linux server
Admin rights and installing the right tools (with no errors), a working edition of (Hisat, Tophat, Cufflinks...etc) rather than a choice of several edition and packages
Getting to embed Genome sequences (like usegalaxy) and choosing the best annotations
Using FTP programs on local machines and Linux server, including the option to transfer files to special directory using linux command line rather than FTP.
I think it would be a great manual for beginners... Unbelievably useful and important...
Maybe somebody can help?