Regarding (2), have you installed bowtie and tophat on your Mac Pro?
Galaxy does not currently automatically install all of the software
needed to run tools (we are working on this through the toolshed, but
at the moment it is a manual process).
Dependencies of various tools included in the distribution are here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jun 11, 2013 at 9:20 AM, Elwood Linney wrote:
> Hello, I will try this again without attachments and hope it gets on the
> list.
>
> I have installed a local instance of Galaxy as a one user in a Mac Pro
> desktop. I got some valuable help from Dannon Baker regarding how to load
> large datasets into it. However I noticed that the Upload file for this
> instance would only go up to the
>
> Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish
> assembly while where as the online version went up to the newer assembly
>
> zebrafish assembly Jul. 2010 (Zv9/danRER7)
>
>
> While I could download newer reference genome in the program from UCSC Main
> table browser
> whenever the local instance offered alternatives for genomes it only went up
> the earlier version
> (Zv8/danRer6) (danRer6) .
>
> I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat,
>
> An error occurred with this dataset: Could not determine Tophat version
> /bin/sh: tophat: command not found Error indexing reference sequence
> /bin/sh: bowtie-build: command not found
>
> So minimally I have two problems that may or may not be related:
>
> 1)The Galaxy-dist that I just installed into a Mac pro does not have the
> latest zebrafish assembly
>
> 2) but more importantly when I try to process groomed datasets through
> Tophat and "Use a built-in genome" as reference it does not allow me an
> option for the reference genome AND if I try to use a reference genome from
> the UCSC download, it won't allow that.
>
> So right now I am stymied--any advice?
>
> Elwood Linney
> Duke University Medical Center
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
> http://galaxyproject.org/search/mailinglists/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
