GMOD/Apollo

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

Julie McMurry

@jmcmurry

I'm going to opt out of this room, but please mention me if you want me to weigh back in.

Nathan Dunn

@nathandunn

will do @jmcmurry ;)

Yating Liu

@Yating-L

is there an alternative way to build the indexes used for name searching and autocompletion, instead of generate-name.pl?

Because I would like to avoid generating a set of static JSON files. Is there a way to just generate one name index file

Yating Liu

@Yating-L

A quick question: is JBrowse-1.14.1 compatible with Apollo? I got error saying "Failed to load resource: WebApollo/main”

@nathandunn

Nathan Dunn

@nathandunn

@Yating-L Not yet. I’m waiting for someone to say “I absolutely need feature X of new JBrowse” . . .

@rbuels started and I had it mostly working here: GMOD/Apollo#1870

Yating Liu

@Yating-L

i see, so the latest JBrowse we can use is 1.12.5?

@nathandunn

Nathan Dunn

@nathandunn

if there is a way to pin the jquery-ui version, or fix the jquery-ui version within JBrowse that would very worth-while

yes

@Yating-L 1.12.5 would be the most recent . . . I’ll fix that in master

Yating Liu

@Yating-L

Thanks! :+1:

@nathandunn

Nathan Dunn

@nathandunn

yeah, I porobalby need to take a week and just finish this out

Scott Cain

@scottcain

@nathandunn did you see my tweet in the thread with Ian and Daniel Lawson about codon highlighting in Apollo? Is it really not possible in Apollo now?

Nathan Dunn

@nathandunn

@scottcain I did not

@scottcain do you have the link to the tweet?

Scott Cain

@scottcain

https://twitter.com/strumpfe/status/1025325725879070720

Nathan Dunn

@nathandunn

should be answered there. Thanks

Scott Cain

@scottcain

@nathandunn I’ll be giving a gmod talk tomorrow and letting the class use the demo Apollo server; it will be around, right? Thx

Nathan Dunn

@nathandunn

@scottcain it seems to be woring, but test

I did bring it down yesterday, so good to let me know

Scott Cain

@scottcain

Yep, I’ve been playing with it. I just wanted to let you know :-)

Nathan Dunn

@nathandunn

hey @scottcain ready your email from me when you have a moment today

if you have time

Cory Maughmer

@MoffMade

@nathandunn this is Cory

Nathan Dunn

@nathandunn

hey @MoffMade

Nathan Dunn

@nathandunn

@MoffMade this is ready for review GMOD/Apollo#1959

Scott Cain

@scottcain

@nathandunn apollo@lists.lbl.gov is the current apollo mailing list right?

Nathan Dunn

@nathandunn

apollo@lbl.gov . . . moved to google groups

@scottcain

Scott Cain

@scottcain

Ah, good, glad I asked.

Nathan Dunn

@nathandunn

Top here: http://genomearchitect.org/

Kaustubh Trivedi

@codekaust

Hello!
I was trying to set up https://github.com/GMOD/Apollo/ using Docker.
I would prefer to run the following command:

Install a latest release to test installation: docker run -it -p 8888:8080 -v /directory/to/jbrowse/files:/data gmod/apollo:latest

What should I pass as
/directory/to/jbrowse/files

Nathan Dunn

@nathandunn

@codekaust it should be the path to your jbrowse directory files. e.g., /opt/apollo/data in this example: https://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#adding-data-to-apollo

Scott Cain

@scottcain

Nice paper that mentions two GMOD projects in the abstract: MAKER and Apollo. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224086

Nathan Dunn

@nathandunn

thanks. I remember Macela asking about it, but I hadn’t had read it in publication yet

Nathan Dunn

@nathandunn

@rbuels / @garrettjstevens . . . hey, was having another thing about Apollo / JB2 integration. As Apollo 2.6.1 server package is part of a mono-repo that also includes JB1, the Apollo / Dojo JS plugin, and the GWT code (everything on the RHS), which is mostly the admin panel. I think it would make the most sense to separate this package and move it to a separate repo as grails 4 (from grails 2.5). In theory you could keep the existing security, but update the swagger package (already done once). Anyway, I know there is some JB2 stuff to work on, yet but we could talk about that on Tuesday.

Robert Buels

@rbuels

Yeah that’s a good catch, let’s talk about it.

Nathan Dunn

@nathandunn

sure . . also, would be useful for me to understand your putative process as well

Nathan Dunn

@nathandunn

@rbuels / @garrettjstevens I added agenda

Robert Buels

@rbuels

:thumbsup:

Robert Buels

@rbuels

@nathandunn garrett isn't going to be there tomorrow, he's off till Thurs

Nathan Dunn

@nathandunn

@rbuels okay. We should still meet if that works. so we are a bit more on the same page with what things look like and some clarification on the Apollo grant. We should be able to loop in Garret next week. . . . should we rename that meeting to the Apollo weekly meeting?

Robert Buels

@rbuels

yes. could you re-do the invite so it's just me you and garrett for now

Nathan Dunn

@nathandunn

:+1:

Nathan Dunn

@nathandunn

@garrettjstevens http://demo.genomearchitect.org/Apollo-staging/WebServices

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