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  • Feb 26 2018 23:40
    nathandunn synchronize #1235
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    Fix cvTerm and alternateCvTerm … (compare)

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Kaustubh Trivedi
@codekaust
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:
Nathan Dunn
@nathandunn
maybe nexxt week we could look at doing a project board? I only have a single linked repo: https://github.com/orgs/GMOD/projects/4
But I’m certain we’ll add more
Actually, I linked some more, but not sure what we should be doing
. . anyway, next week
Garrett Stevens
@garrettjstevens
@nathandunn I'm getting an access denied error when trying to download "Honeybee without BAM" data from https://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html
Nathan Dunn
@nathandunn
okay, one minute here
sorry, was off the morning
@garrettjstevens these are fixed now . . sorry, the bucket policy must have changed at some point
Garrett Stevens
@garrettjstevens
Thanks!
Nathan Dunn
@nathandunn
FYI, no meeting next week
Robert Buels
@rbuels
@garrettjstevens @nathandunn want to have our little check-in meeting?
i'm also fine with skipping it ;-)
Garrett Stevens
@garrettjstevens
I think Nathan said last week he was planning on not having it
Robert Buels
@rbuels
bleh then should have updated the calendar :-p
Nathan Dunn
@nathandunn
Sorry thought I did .. sometimes events are sticky
Have a merry Xmas you two
Let’s plan to talk next in the new year
Nathan Dunn
@nathandunn
I’m working today, but confirming that we are meeting next week and not this week.
Nathan Dunn
@nathandunn
I used to work there. The tricky part is that there is only one European developer.
Not sure the status, but I can ask.
But he is also a Spring dude.
I’m not sure if they are the staying or going list.
Nathan Dunn
@nathandunn
Was thinking @garrettjstevens as you develop the IO piece for talking to the backend of Apollo, if you are able to split it into its own library, that is something I can actively work putting together, as well since we’ve had to do that in a few other pieces.
Nathan Dunn
@nathandunn
@garrettjstevens / @rbuels : I added issues from todays call: (3) https://github.com/GMOD/jbrowse-plugin-apollo/labels/BRC4 (4) https://github.com/GMOD/Apollo3Server/labels/BRC4 .. they are all on the same project board: They are added to this project board: https://github.com/orgs/GMOD/projects/4 . . . not permanent, but wanted a placeholder.