Proteomics: Old EMBOSS download used by Galaxy-P no longer available, update to 6.6.0. (This probably needs to be updated other places as well).
Proteomics: ms2preproc disappeared from other site. Found a new download. Small updates to install procedure.
Fill in some missing gaps between Ubuntu and CentOS/SL (base R). Add documentation pointer to fill in some more manually (rpy and scipy).