Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
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
    wafflebot[bot] labeled #1235
  • Feb 26 2018 23:26
    wafflebot[bot] unlabeled #1235
  • 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
    nathandunn milestoned #1864
  • Feb 24 2018 07:31
    nathandunn commented #1864
  • Feb 24 2018 07:17
    nathandunn synchronize #1864
  • 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
    nathandunn synchronize #1864
  • Feb 24 2018 01:05
    deepakunni3 review_requested #1864
  • Feb 24 2018 01:05
    wafflebot[bot] labeled #1864
Yating Liu
@Yating-L
@scottcain Things will be different when you uploading to CyVerse. Besides transfering the files, each file need to be registered in the database. So more files, more database updates…That’s my understanding. So it takes much longer than normal platform with numerious files
Scott Cain
@scottcain
@Yating-L yuck. I guess you get what you pay for :-/
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