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Question: Installing standalone Galaxy with reference geneome
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gravatar for simplitia
4.6 years ago by
simplitia • 0
United States
simplitia • 0 wrote:

Dear all, newbie question here. 

So I installed Galaxy on my linux box.  When I try to upload a dataset I see a drop down for reference genome; I chose this and was able to upload successfully.  However, when I tried to use a tool that I installed, TopHat Illumina, the place where the choose reference genome does not contain any of the genome listed in the upload section. Its just an empty box.  Question I have is how do I install a reference genome (ie mouse mm9) so that I can get it to work with TopHat.  I'm a bit confused since it was present in the upload section but not here, so maybe I don't need to install the reference genome?  

 

thank you very much!

Ahdee
tophat bowtie galaxy install standalone • 1.4k views
ADD COMMENT • link •
modified 4.6 years ago by Dannon Baker ♦ 3.7k • written 4.6 years ago by simplitia • 0
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gravatar for Dannon Baker
4.6 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

You do need to install reference genomes on your own.  As they can be very large, we don't ship them with Galaxy.  See https://wiki.galaxyproject.org/Admin/DataPreparation for more details.

Hope this helps!

-Dannon
ADD COMMENT • link written 4.6 years ago by Dannon Baker ♦ 3.7k

Thanks Dannon: I will check this out.  I even found compile index files for Bowtie link below in case someone else needs it. 

ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/

ADD REPLY • link written 4.6 years ago by simplitia • 0
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