[Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

Hi all,

I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) 
and added 2 species (well, different cultivars) by doing the following:
bin/prepare-refseqs.pl --out data/nipponbare --fasta 
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures 
--trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
bin/generate-names.pl --out data/nipponbare

bin/prepare-refseqs.pl --out data/arc --fasta 
source_files/magic_16/oryza_sativa_arc.fa
bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures 
--trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
bin/generate-names.pl --out data/arc

Then I edited the jbrowse.conf file as explained in 
https://jbrowse.org/docs/dataset_selector.html to have:
dataRoot = data/nipponbare
[datasets.nipponbare]
url = ?data=data/nipponbare
name = Nipponbare
[datasets.arc]
url = ?data=data/arc
name = ARC

And all seems to work fine, except that I don't see the dropdown to 
switch datasets, so I can't actually see the ARC dataset. Although I 
have by messing around with jbrowse.conf and tracks.conf gotten it to 
work, but at this point I've left it out.

However, the issue I'm having is actually with Apollo. I have the docker 
instance of apollo running and it seems to be fine as configured in a 
systemd unit file:
ExecStart=/usr/bin/docker run --rm --name %n \
         -e APOLLO_PATH=apollo \
         -v /data/www/panoryza/jbrowse/data:/data \
         -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
         -v 
/data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
         -p 8887:8080 \
         gmod/apollo:latest

Adding Nipponbare as an organism with "Directory" /data/nipponbare works 
fine and I can see the tracks I've added.

Now, here is where the issue I have starts. If I edit the 
data/nipponbare/tracks.conf file as shown in the dataset selector 
documentation above:
[general]
dataset_id = nipponbare

Apollo then shows the following error:
Error message(s):
     TypeError: Cannot read properties of undefined (reading 'name').

Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
Now, the error only appears in apollo, jbrowse works fine with the edits.

I'm a bit confused about how this should be configured to work. I 
actually have 14 more "species" to add, but waiting till I at least get 
it working with one. The documentation isn't clear to me on the 
difference between adding the datasets to jbrowse.conf vs 
data/tracks.conf vs data/(species)/tracks.conf.

Please let me know if you need any more information.

Thanks,
Justin

-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: jus...@or...                   *
*                                                        *
**********************************************************