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GMOD/Apollo

Genome annotation editor, with a Java servlet backend and a Javascript client that runs in a web browser as a JBrowse plugin

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Repo info

Activity

Feb 26 2018 23:40

nathandunn synchronize #1235
Feb 26 2018 23:40

nathandunn edited #1235
Feb 26 2018 23:33

nathandunn assigned #1235
Feb 26 2018 23:32

nathandunn synchronize #1235
Feb 26 2018 23:26

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Feb 26 2018 23:26

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Feb 26 2018 23:26

nathandunn synchronize #1235
Feb 26 2018 10:55

epaule commented #1863
Feb 24 2018 17:25

deepakunni3 commented #1864
Feb 24 2018 07:36

wafflebot[bot] unlabeled #1864
Feb 24 2018 07:36

nathandunn on master

Fix cvTerm and alternateCvTerm … (compare)
Feb 24 2018 07:36

nathandunn closed #1864
Feb 24 2018 07:36

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Feb 24 2018 07:31

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Feb 24 2018 07:09

nathandunn on master

pinging build (compare)
Feb 24 2018 06:53

wafflebot[bot] assigned #1864
Feb 24 2018 06:53

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Feb 24 2018 01:05

deepakunni3 review_requested #1864
Feb 24 2018 01:05

wafflebot[bot] labeled #1864

Deepak

@deepakunni3

ah, yes. We should add this to the agenda for Thursday

Nathan Dunn

@nathandunn

agreed

Robert Buels

@rbuels

@nathandunn oh this channel exists!

Nathan Dunn

@nathandunn

I here

Dan Keith

@DoctorBud

I'm just a fly on the wall here... Pay me no mind.

Nathan Dunn

@nathandunn

He’s on to us!

Nathan Dunn

@nathandunn

Apropos @DoctorBud the genome feature widget is bein refactored to not have any react components in the test or the demo, so hopefully will clean things up

Robert Buels

@rbuels

@nathandunn @deepakunni3 OK if I configure Gitter to watch the GMOD/Apollo repo and issues for activity messages

commits and whatnot

Deepak

@deepakunni3

@rbuels Yes, that would be useful to keep track of development :+1:

Robert Buels

@rbuels

ok done. events in the GMOD/Apollo repo should appear in the sidebar now

Nathan Dunn

@nathandunn

Please!

Yating Liu

@Yating-L

@nathandunn I removed the gene lines from GFF3 and generated GFF3Tabix track. But there are a few CDS do not show. Is this a known issue? Or it has been solved?

Screen Shot 2018-04-05 at 9.57.24 AM.png

Nathan Dunn

@nathandunn

@Yating-L I’m not sure. If the CDS parent is the exon or the gene instead of the mRNA that could be a problem. Mostly it depends on how its created. Can you send your samples before and after?

I’m assuming this is just for the HTML version?

Yating Liu

@Yating-L

HTMLFeatures, yes

Augustus.sorted.filtered.gff3

Yating Liu

@Yating-L

Augustus.sorted.gff3

@nathandunn here are the gene prediction output file, before and after filtering gene lines

Nathan Dunn

@nathandunn

@Yating-L there are no exons (which is fine). Are you saying that it is not showing some of the specified CDS’s?

Robert Buels

@rbuels

@nathandunn is this the use case you're working on in your gff3tabix pull req so that it works out of the box?

Nathan Dunn

@nathandunn

@rbuels I thiknk so

Yating Liu

@Yating-L

@nathandunn yes, some CDSs are not showing

Nathan Dunn

@nathandunn

@Yating-L this is with the HTMLFeatures?

I’m guess it is

so, the answer to your question is yes @rbuels

Yating Liu

@Yating-L

@nathandunn I think so. I tested on two GFF3. Canvas renders correctly

but HTML missing some subfeatures

Robert Buels

@rbuels

which data store were both tests using? GFF3Tabix?

Yating Liu

@Yating-L

"JBrowse/Store/SeqFeature/GFF3Tabix"

Nathan Dunn

@nathandunn

yeah, they both use the same store. The difference is when the Canvas redners, they just render one on top of another and it works. With HTMLFeatures, you can’t do that with divs and so it blocks the other one out

Yating Liu

@Yating-L

is this solvable?

Robert Buels

@rbuels

is there a reason that you guys can't just use canvasfeatures? i've been hoping since 2013 to deprecate htmlfeatures

is it cause of apollo needing to drag the features around

Nathan Dunn

@nathandunn

@rbuels Part of it is dragging the features, an important feature of Apollo. The other reason is highlighting edges.

Nathan Dunn

@nathandunn

I guess the two questions are: @Yating-L can you use the JSON version? and @rbuels how much work would it be to fix the HTMLFeatures?

Robert Buels

@rbuels

i'm going to work on fixing the htmlfeatures, cause it is already on the 1.14.0 milestone

Nathan Dunn

@nathandunn

A couple of reasons to fix it as well: (1) the more users we have using GFF3Tabix, the fewer users we’ll have to transition with the newer JBrowse, and (2) handling the JBrowse JSON files has been problematic because of the large number of files versus tabix

@rbuels . . .. looking for proper emojis

:fire: :clap: :sparkles:

:rocket:

@rbuels Do you have colin and my half-working attempts?

not sure if they would be helpful or not

Yating Liu

@Yating-L

@nathandunn we want to use tabix because we want to upload jbrowse to CyVerse Data Store. JSON version generates too many files, which takes too long to upload

Nathan Dunn

@nathandunn

thanks @Yating-L . . @rbuels , who is much more capable than I, is going to work on this. Thank you very much @rbuels

Yating Liu

@Yating-L

And HTMLFeatures is useful for our team because they want the dragging features and highlight edge features

Robert Buels

@rbuels

@nathandunn do you have everything in your pull requests?

if not, just tell me what other branches there are and I'll take care of weaving them all together

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