Use explicit paths to all important program used in pipeline
Eg. Tophat and bowtie. It is already possible to set a path in the reggie-ogs-hosts.xml file for most of the programs, but tophat also uses bowtie and will look it up in the PATH, which may or may not be the same as in our configuration.
The default configuration file should include complete paths to tophat and bowtie. The generate script for alignment should extend the PATH with the path to bowtie.