Hi Elwood, I am in a similar situation. Our lab is trying to connect Bowtie version 1 to our local Galaxy framework. We are slowly making progress with the help of people at seqanswers.com You are welcome to review the thread I started at http://seqanswers.com/forums/showthread.php?t=31047 since it might contain information that relates to your situation. If you do not receive help from this mailing list, I recommend posting your question at seqanswers.com Good luck!

Message: 22 Date: Thu, 20 Jun 2013 11:45:20 -0400 From: Elwood Linney <ellinney@gmail.com> To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance Message-ID: <CAC-Zp0yDhx5Dr0ffdtRB-h=uLZR5UZaBkyVh+8riFYemNmwVnw@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"

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