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Question: Reference Genomes At Local Instance Of Galaxy
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gravatar for Yang, Yanming
6.7 years ago by
Yang, Yanming • 10
Yang, Yanming • 10 wrote:
Hi, I have just installed a Galaxy instance at my local machine and uploaded some sequence data into it. But, when I tried to use some NGS tools which need reference genome, I found the selection window was empty. I wonder how to get a reference genome data (e.g., hg19) incorporated into the local Galaxy. Any help will be greatly appreciated. Thanks! Yanming Yang
galaxy • 3.2k views
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modified 15 months ago by laurent.fournier • 10 • written 6.7 years ago by Yang, Yanming • 10
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gravatar for laurent.fournier
15 months ago by
laurent.fournier • 10
GIGA Research Center
laurent.fournier • 10 wrote:

Hello Jen,

I am actually trying to install a local instance of galaxy on my work's cluster. Everything runs smoothly except for reference genome therefore here i am.

https://galaxyproject.org/Admin/NGS%20Local%20Setup do not exist anymore, can you reroute me somewhere in order to do this ?

Best regards, Laurent.
ADD COMMENT • link written 15 months ago by laurent.fournier • 10
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gravatar for Jennifer Hillman Jackson
6.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Yanming, To set-up native NGS data indexes, please see the instructions in this wiki: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Uploading data into a history in fasta format will allow that dataset to be used as a custom reference genome with most tools, which is another option. This wiki explains how the Custom genome method works: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes Hopefully this helps! Best, Jen Galaxy team
ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
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