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  • Feb 26 2018 23:40
    nathandunn synchronize #1235
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    nathandunn on master

    Fix cvTerm and alternateCvTerm … (compare)

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    pinging build (compare)

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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?
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
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
Nathan Dunn
@nathandunn
quick note . . was looking at moving Apollo 2 to Grails 4 . . then it occurred to me you have to switch to use Java 10+ . . which breaks the compilation of GWT . . . so I would just use what is there at this injucture
Robert Buels
@rbuels
sounds good to me :thumbsup: