Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

I haven't evaluated the whole post here, but note that Apollo automatically
creates a dataset selector from assemblies that you configure through that
Apollo interface


-Colin

On Wed, May 25, 2022 at 12:21 PM Justin Elser <jus...@or...>
wrote:

> 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...                   *
> *                                                        *
> **********************************************************
>
>
>
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