I've recently updated a tutorial website I put together for a MSc project, it's only a starting point but may be useful. After some university re-structuring it has had to be moved to below link:

http://elvis.misc.cranfield.ac.uk/CUBELP2/

I can't update it any more as don't have university access so will become more dated in time but hopefully useful for the short term.

It consists of RNA-seq, ChIP-Seq, Genome assembly, SNP calling tutorials contrasting galaxy and command line methods in most cases.