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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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    pinging build (compare)

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scottcain @scottcain congratulates himself for talking about using CyVerse but never getting around to it.
Yating Liu
@Yating-L
It is free, so great place for long-term storage
I don’t know if there’re better options
Scott Cain
@scottcain
Probably not for free—though you might look into Google. I know somebody at Google Cloud who is there to promote it for use with genomics data and probably has free stuff to give out.
Nathan Dunn
@nathandunn
@scottcain I think there are also grant obligations to use the Cyverse platform. This is true for a number of users within the GMOD. I’m not sure if this is because the idea is that each object can have an individual ID.
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?
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