Problem with combination track, not working

[armaos]

Hello, I am kind of newbie in this so apologies if i ask something easy. I am struggling to solve a problem similar to 351

I have JBrowse 1.15.1 with JBconnect running on an AWS instance. I am using Google Chrome as browser.

My problem: I have loaded my tracks (bam/bigwig etc) I have tried also what is suggested here 1361 But no luck.

When i drag and drop to the combination track, even if it turns "green", nothing is loaded as track, however in the config of the combination track i see the key of my add track..

Interestingly i noted 2 things:

1. when I load 2 tracks, the dialog asks me for the function. I see this Javascript appear.

2. in the browser console, when i load a track i see these errors:

Is that an issue? Do i do anything wrong.

Thank you very much. A.

[cmdcolin]

what types of tracks are you combining?

[armaos]

Hello,

this happens when i try to load any track. Even When trying to load the very first track I face the same problem.

for instance if I load any of them following, the problem exists:

"storeClass": "JBrowse/Store/BigWig", "type": "JBrowse/View/Track/Wiggle/XYPlot", "urlTemplate": "../bigWig/SRR1207056.bw",

or

"storeClass": "JBrowse/Store/SeqFeature/NCList", "trackType": "null", "type": "JBrowse/View/Track/HTMLFeatures",

or

"storeClass": "JBrowse/Store/SeqFeature/NCList", "trackType": "JBrowse/View/Track/HTMLFeatures", "type": "JBrowse/View/Track/HTMLFeatures",

thank you. A

[cmdcolin]

are you able to reproduce the issue on our sample data browsers?

current version

https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9899..34156&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2Cvolvox-sorted-vcf%2Cvolvox-sorted_bam_coverage%2Cvolvox-sorted_bam&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1

version you mention you are using

https://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgA%3A9899..34156&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2Cvolvox-sorted-vcf%2Cvolvox-sorted_bam_coverage%2Cvolvox-sorted_bam&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1

[armaos]

I loaded one of my bam files in to https://jbrowse.org/code/JBrowse-1.15.1... (Track -> Open track file or URL) and the combination track was responsive. So the error was not reproducible.

I also downloaded one of the sample bam files form the https://jbrowse.org/code/JBrowse-1.15.1... and loaded in my instance and again the combination track was not working. Same problem as i describe above. I drag and drop but nothing happens. So its a matter of my instance and not of the files or the jbrowse version if i understand well. DO the errors pasted above help you trace the origin of the problem? thank you again

[cmdcolin]

Not sure I can tell. Do you have any plugins or customizations? Is it running in webapollo or anything like this?

[armaos]

@cmdcolin thank you for looking into this! As for your question: I am not running Apollo. The only custom plugins are the blast and jblast plugins. And to be honest I havent touched any of the Jbrowse configurations.. :/

the error comes from the jbrowse/src/JBrowse/View/Track/Combination.js

storeType is typeof 'function' and more specificaly:

function() { var what, a = arguments, L = a.length, ax; while (L && this.length) { what = a[--L]; while ((ax = this.indexOf(what)) !== -1) { this.splice(ax, 1); } } return this; }

[cmdcolin]

CC @enuggetry would you be able to check this out under jblast?

[armaos]

I have some news here. @cmdcolin I found out that the issue is the JBlast plugin . when i remove it, the combination track seems to work... Any workaround? Write blast from scratch maybe? or switch to JBrowse2 i think.

[cmdcolin]

If you wanted to "roll your own" blast integration, there is an example here with sequenceserver https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse

[cmdcolin]

Don't have a jbrowse 2 example of this yet but would be great to have!