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monarch-initiative / monarch-ui

The previous version of the Monarch Initiative website
https://previous.monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
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Fix broken jbrowse link #346

Closed kshefchek closed 4 years ago

kshefchek commented 4 years ago

Currently the genome feature component links to broken jbrowse pages:

For example: https://monarchinitiative.org/gene/MGI:98297 links to: http://jbrowse.alliancegenome.org/jbrowse/index.html?data=data/Mus%20musculus&loc=5:28456815..28467256

Long term we'll want to boot up our own instance of jbrowse for monarch, but the meantime we should link the alliance version at https://www.alliancegenome.org/jbrowse/

monicacecilia commented 4 years ago

As of 2020-07-27, https://monarchinitiative.org/gene/MGI:98297 no longer links to that JBrowse location. See screenshot below.

Screen Shot 2020-07-27 at 12 39 17 PM

monicacecilia commented 4 years ago

This is what that location looks like right now at AGR: https://www.alliancegenome.org/jbrowse/?data=data%2FMus%20musculus&tracks=Variants%2CAll%20Genes&highlight=&lookupSymbol=Shh&loc=5%3A28450678..28473253

jen-martin commented 4 years ago

As of 2020-07-27, https://monarchinitiative.org/gene/MGI:98297 no longer links to that JBrowse location. See screenshot below.

This was fixed with PR 351 but the larger issue of what to do when mygene fails to get coordinates for organisms in jbrowse still remains.