Re: Questions on uploading tracks to Apollo

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Re: Questions on uploading tracks to Apollo


On Oct 17, 2020, at 7:55 AM, Abhijit Sanyal <[hidden email]> wrote:

Sure Nathan. No problem. I have another question for you.

 The admin at our institution installed Apollo via docker. But does not know where to look for the jbrowse scripts for loading the gff3 data. I see two folders created. 

docker-apollo/ and compose-apollo/

Which should I take to search for the scripts? I can send you screen shots if you want.


I would just install JBrowse and use the scripts from that if possible.  Should be in the bin directory. 

You have a few options:

1 - install jbrowse directly from a download and use what is in the bin directory

2 - install jbrowse via docker:

3 - use what is in the docker Apollo: /var/lib/tomcat9/webapps/ROOT/jbrowse/bin 

. . you would have the mount the directory in the case of 2 or 3 to use it externally

On Sat, Oct 17, 2020 at 8:19 PM Nathan Dunn <[hidden email]> wrote:
Do you mind if I reply to this on the Apollo groups so that others may benefit from our conversation?


> On Oct 17, 2020, at 6:05 AM, Abhijit Sanyal <[hidden email]> wrote:
> Hi Nathan,
> Just a few questions regarding upload of tracks to Apollo from the desktop
> 1) I have gff3 files to upload, however the options I see are "GFF3 JSON", "GFF3 JSON CANVAS", "GFF3", "GFF3 Canvas". Which one should I pick? I could not find a help page on this. Maybe I missed something?

I would use GFF3 to start (you can always delete or add with a different type later). 

The different types are referenced badly here. 

GFF3 uses the native GFF3 adapter, whereas JSON uses the “” which would be recommended for long and dense GFF3 tracks, converting it into a modified file format with histograms.  

> 2) What does the "category" field stand for? I do not know what to put here.

You can leave this blank.  If you want a “section” in our track you put something in here: 

> 3) I have the following types of gff3 files for genes, repeats, ncRNA. For genes I will use "--type mRNA". What to use for the other two?

I would use whatever is in column 3 that you want to see, which is what it does the filter be.   Sometimes I have to play with it a bit to see what I want.  

The JBrowse community and doc might be helpful here as well.  

Sample files would help here if you can’t make this work. 

Hope all this helps. 


> Thanks
> Abhijit

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