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 <ellin...@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+8rifyemnmw...@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
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