GMOD/Apollo

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

Nathan Dunn

@nathandunn

I’ve talked to other groups who’ve had the same problem as @Yating-L The problem is worse for the sequence files, but backups, data creation, etc. becomes problematic with lots of data.

@rbuels you can also reproduce the problem using the Volvox GFF3Tabix I added for canvas

Scott Cain

@scottcain

No, I mean uploading to S3; I run flat file_to_json on a local machine and then aws s3 cp —recursive to move the files to my S3 bucket. I do this for gene data for several species at once (yeast, worm, fly, zebrafish, mouse, rat and human) and it takes under an hour. To be fair, copy is a lot faster than rsync, and I only do the sequence data once even though I update feature data often. In this context, removing old remote data and copying the new local data up to the cloud makes sense and rsync isn’t really needed. of course, I also compress all of my tracks :-)

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?

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

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