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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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add ability to import GA4GH endpoints #518

Closed nathandunn closed 5 years ago

nathandunn commented 9 years ago

should be able to import GA4GH endpoints:

https://github.com/ga4gh/server

reference: http://ga4gh-reference-implementation.readthedocs.org/en/latest/demo.html

nathandunn commented 9 years ago

The JS code is here: https://github.com/acthp/ga4gh-rxjs

nathandunn commented 8 years ago

Not sure if this is consistent with becoming a GA4G4 end-point:

https://docs.google.com/document/d/1ITQMvA0HEqXirPvQglE8bwk5W1GXYkPGb_cCz0NLnxE/edit#

cmungall commented 8 years ago

Reference server for 1k genomes here: http://1kgenomes.ga4gh.org/

the iPython notebook is a good overview

Obviously the 1k genomes would be good to have for the human server

cmungall commented 8 years ago

Discussed this with @selewis, priority should be increased

nathandunn commented 8 years ago

Okay . . . well, our next release is 2.0.3 and then 2.0.4 . . but we can do it next thing after variant annotation comes out.

nathandunn commented 8 years ago

FYI @monicacecilia . . . we should figure out where this goes in the queue

monicacecilia commented 8 years ago

@cmungall copy that. @nathandunn : goes after variants viz. & annot., which goes after coordinate transformation. So after, after... This now has more priority but does not trump Spring'16 priorities from grant.

nathandunn commented 8 years ago

@monicacecilia K . . I will leave the milestone as it is then.

monicacecilia commented 8 years ago

p.s: 1k genomes does not mean 1k tracks. It means 1 population track with background data & viz. of allele frequencies.

cmdcolin commented 8 years ago

I think since they allow "range queries" on genomic coordinates, it makes getting the feature data pretty easy. Probably similar to having the myvariant.info tracks.

nathandunn commented 8 years ago

Right. The data can be cut in many different ways. We do have it .. I think we didn't load it until we had a more concrete use case for it.

Nathan

On Apr 26, 2016, at 2:12 PM, Monica Munoz-Torres notifications@github.com wrote:

p.s: 1k genomes does not mean 1k tracks. It means 1 population track with background data & viz. of allele frequencies.

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cmdcolin commented 8 years ago

In addition to the ipython notebook, they had another demo of just accessing the API in javascript http://htmlpreview.github.io/?https://raw.githubusercontent.com/david4096/bioapi-examples/master/1kgenomes.html

I think this example is querying data from a subset of 1kg. In any case, I'd probably just access the API directly like that example page rather than use the rxjs library. It probably doesn't hurt but it's a pretty tiny accessory library.

nathandunn commented 8 years ago

https://github.com/ga4gh/schemas/tree/protobuf/src/main/proto/ga4gh

An initial implementation:

http://1kgenomes.ga4gh.org

cmdcolin commented 8 years ago

I was just poking around and made a GA4GH data viewer as a proof of concept pretty quick. Here is a little demo for both the myvariant viewer and a GA4GH track.

Test browser here http://cmdcolin.github.io/jbrowse/?loc=chr1%3A120471622..120472035&tracks=MyVariant.info%20clinvar%2CGA4GH%201kg%2CMyGene.info&highlight=

The GA4GH variants have really long ID names so it's just printing those out as is

nathandunn commented 5 years ago

I'm going to say that this has been done as a part of @cmdcolin 's JBrowse plugin:

https://github.com/elsiklab/ga4ghviewer

We can expand on this if we get further requirements. 👍