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Question: No display link to UCSC with sacCer3
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gravatar for david.a.morais
3.1 years ago by
david.a.morais • 110
Canada
david.a.morais • 110 wrote:

Hi All,

 

I noticed the on my local Galaxy (most recent version), when I load a yeast, sacCer3 dataset the link 'display in UCSC main' is not showing.
It works well with sacCer1, though.

I checked and I have the sacCer3.len file. I also used the data manger to create a new dbkey.loc entry that was more similar to what is displayed on the Galaxy main 'S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)', but that also did not produced any results.

In my .ini config file that is the set up to display servers

display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu

 

Finally I have all the genome/sacCer3/ data like  sam, bowtie, bwa  indexes, seq/ dir (sacCer3.2bit and  sacCer3.fa). They can all be seen by Galaxy.

Can someone please help me, to find out why 'display on UCSC main' is not showing?

Thanks
ucsc visualization • 607 views
ADD COMMENT • link •
modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by david.a.morais • 110
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The genome sacCer3 should be added to the tool-data/shared/ucsc/builds.txt (or tool-data/shared/ucsc/builds.txt.sample if that is still in use)

Other external display sites configuration files can also be updated. This is a list of where sacCer2 has been added - sacCer3 could also be added (plus any other genomes that need to be, as long as they exist in your Galaxy server and the 3rd party server).

https://github.com/galaxyproject/galaxy/search?utf8=%E2%9C%93&q=sacCer2

I opened a ticket for our team to consider updating the builds.txt.sample to match the most complete, current version in use on http://usegalaxy.org. Progress on the enhancement request can be followed here: https://github.com/galaxyproject/galaxy/issues/981

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks a lot Jennifer,

I looked into the tool-data/shared/ucsc/builds.txt and sacCer3 was there but it was not in the tool-data/shared/ucsc/ucsc_build_sites.txt, so it was just add it there e voila! the display was back.

Thank you very much!!!

ADD REPLY • link written 3.1 years ago by david.a.morais • 110

Great to know. The config file you reference is another one for external display that needs to be set up (and I thought it was by default). But, glad all working now! Jen

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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