Hello again,
I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a  server or doing full time bioinformatics, but there are some of us computer numbskulls  that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup.
I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely
NGS: RNA Analysis
1)  Tophat for Illumina
tophat (1.3.3-1.4.0) with bowtie + bowtie indexes
2)  Cufflinks
cufflinks (1.3.0-2.1.1)
3)  Cuffcompare
cufflinks (1.3.0-2.1.1)
4)  Cuffmerge
cuffmerge (1.3.0-2.1.1)
5)  Cuffdiff
cuffdiff (2.1.0-2.1.1)
I have transferred the galaxy framework in a work/galaxy-dist   pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin.  For the next year at least my needs with be just the RNA analysis tools above.
Any help will be greatly appreciated.
My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause

Sincerely,
Elwood Linney