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Re: [Gmod-ajax] Dataset selector in apollo
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From: Colin <col...@gm...> - 2022-05-25 23:52:14
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The logs that are probably most helpful are the "JavaScript console" or developer console from chrome or firefox e.g. https://balsamiq.com/support/faqs/browserconsole/ On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...> wrote: > We may just use Apollo to serve both, but thought I might give it a try to > see about JBrowse. > > I am attaching the output I get when I run the docker container with "-e > WEBAPOLLO_DEBUG=true". > > The blank lines are in between it working and not working. IE, lines 1-483 > are the initial startup and navigating to the site with Apollo working as > expected. Lines 487 on are after changing data/nipponbare/tracks.conf to > have: > [general] > dataset_id = nipponbare > > I do notice that after the change it is trying to open > /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run > (line 579) where it isn't before. I don't understand why it would be > looking for the sample data at all. I never loaded it as a track or > anything. > > I also notice for the initial load where it works that it is complaining > about the mime_type for .bam files. I did alter the .htaccess for the > jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly > enough, the bam track does load fine in Apollo where it didn't in JBrowse > until I made the change to .htaccess. > > If you meant some other logs, please let me know how to get those and I > will send them to you. > > Thanks, > Justin > > On 5/25/22 2:18 PM, Colin wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > One option is to use Apollo to serve your jbrowse instances, Apollo can > serve public jbrowse instances so you may not need to configure jbrowse > separately > > > If you do want it separate, then we would probably need to debug that > error. If you have the stack trace from the developer console, it might > narrow down exactly where the error comes from. If the stack trace is > minified and hard to read, can possibly use a "dev" version of jbrowse if > it is too unreadable since it does not minify the builds! > > > > -Colin > > On Wed, May 25, 2022 at 1:03 PM Justin Elser <jus...@or...> > wrote: > >> Yeah, so I guess the problem is that if I don't add the "dataset_id" to >> each data/(species)/tracks.conf file, apollo works fine, but then I can't >> get the dataset selector in jbrowse. As I have it right now, Apollo is >> fine, but I have no way to switch to a different dataset in JBrowse. >> >> >> I was messing around with jbrowse.conf, data/tracks.conf, and >> data/(species)/tracks.conf, and was able to get a list of the species under >> the "Genome" tab. But if I don't have anything in >> data/(species)/tracks.conf, I don't. However, if I do add it like in the >> documentation, the species are listed under there: >> >> But then, apollo breaks: >> >> >> So, I guess I need to get the dataset_selector working in JBrowse, while >> not breaking Apollo. >> >> I hope that clears it up more. >> >> Thanks, >> Justin >> >> On 5/25/22 11:50 AM, Colin wrote: >> >> [This email originated from outside of OSU. Use caution with links and >> attachments.] >> 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... * >>> * * >>> ********************************************************** >>> >>> >>> >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> >> -- >> ********************************************************** >> * * >> * Justin Elser * >> * Computational Biology Research Associate * >> * Dept. of Botany and Plant Pathology * >> * Jaiswal Lab * >> * Oregon State University * >> * * >> * email: jus...@or... * >> * * >> ********************************************************** >> >> > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Research Associate * > * Dept. of Botany and Plant Pathology * > * Jaiswal Lab * > * Oregon State University * > * * > * email: jus...@or... * > * * > ********************************************************** > > |
