Question: How to display in non UCSC genome browsers
gravatar for jsarro
18 months ago by
jsarro10 wrote:

Were are testing passing files to a genome browser on our galaxy instance. We have updated the galaxy.ini file and apache code to accept the server from the genome browser server. The option to display, however, is not appearing. We are wondering if there could be a problem with the genome matching up? For example when I upload a data file on the instance, the file does not automatically show a display option for the ucsc browser. If I update the file settings and change the Database/Build to a preloaded genome then the display option of ucsc appears. So it would appear that in order to display, a valid genome must be in use. We have downloaded the genomes of and uploaded them to our instance and have created database keys and indexes this way. These are the same genomes in the genome browser but perhaps we are doing this wrong, in that the genome browser is not recognizing our genomes stored in data manager (or vice versa). Does anyone have any experience doing this, or have an idea to fix this issue/a different method of doing this?

display • 633 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by jsarro10
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The documentation for this is a bit outdated, so following it exactly is not advised, but here it is for reference:

Advice from the team:

  • Add the new external display application to the tool_conf.xml file
  • Model the entry after the functioning UCSC display application already present
  • Matching "dbkey" database assignment metadata is important, so make sure these are a match

If you have more problems, please post back your tool_conf.xml file with the entry and our team can help. A gist or other link that preserves formatting would be a good way to do that. Any sensitive content can be generalized, in this or any other shared data.

Thanks and let us know how this works out! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k

Thank you so much for your reply, Jennifer. We have a tool_conf.xml.main file but I do not see any display info. I am looking in the config directory of the main galaxy directory, I hope this is the right place.

I have pasted our file on git

Can I just add a section like in the link you pasted above? If so does it belong in the <toolbox> or does a new section need to be created. Additionally, if it is easier can I just set up a way to paste a link of a file into the genome browser and have it accept it? I am trying to do that as well but getting a 401: Authorization Required error, even though we edited the galaxy.ini file and apache code.

ADD REPLYlink written 18 months ago by jsarro10

Hum, something is not right in the instructions I passed on. I'm am reviewing plus getting more feedback. More soon! Jen

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
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