Hi Michael,

Thanks for reporting this, sounds like an older, incorrect, config file is in place. And this can be fixed.
I will be going into the genomes area and re-verifying current builds and other built-in data/indexes shortly.


Galaxy team

On 10/10/13 1:56 PM, Court, Michael wrote:



I minor annoyance that I had found with the current implementation of “Tophat for Illumina (version 1.5.0)” in the public usegalaxy.org site:


When you submit sequences for alignment, the dropdown list of available genomes gives 2 dog genome choices – BUT both are labeled the same – “Dog(Canis lupus familiaris): canFam2”.


After trial and error I found that the second (lower on the list) choice is actually “Dog(Canis lupus familiaris): canFam3.1”.


Hopefully this can be corrected at some point – maybe when the next release comes out from the Broad.






Michael H. Court, BVSc, PhD, Diplomate ACVA

Professor and William R. Jones Endowed Chair

Individualized Medicine Program

Pharmacogenomics Laboratory

Department of Veterinary Clinical Sciences

College of Veterinary Medicine, Washington State University

100 Grimes Way, Pullman, WA 99164-6610

Office: 509-335-0817   Cell: 774-287-7082  Fax: 509-335-0880

michael.court@vetmed.wsu.edu      www.vetmed.wsu.edu




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:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Jennifer Hillman-Jackson