Question: No display link to UCSC with sacCer3
0
gravatar for david.a.morais
2.6 years ago by
Canada
david.a.morais110 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 • 484 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by david.a.morais110
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k

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 REPLYlink written 2.6 years ago by david.a.morais110

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 REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k
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