I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink suite
to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to introduce
my large datasets on the some computer into Galaxy through Admin changing
some permissions

but my minimal knowledge of unix commands and tricks has me stymied

Question:
If my primary purpose is to use this local instance for the analysis of
RNAseq data within my lab, what is the simplest way of connecting the
programs to the Galaxy framework?

While from reviewing info on the Galaxy website I am only guessing that
adding them to $PATH might be the easiest way for me to do this (but I am
not exactly sure what this means or specifically how I would do it in my
case).  However, I do initiate the running of Galaxy by sh run.sh on my
terminal and visualizing things via my localhost port.  There is some
indication from the wiki I found that this might not be good for a system
initiated by sh run.sh    .

[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under
"Local Jobs"

I would appreciate any specific advice on this.

Sincerely,

Elwood Linney
DUMC
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