Adding BigWig files on MultiQuantitative track

[rshakhb10]

Hi! I am trying to add bigwig files under MultiQuantitative Track under "bigWigs" keyword on json. The files are stored locally on a persistent storage. However, jbrowse fails to load them...
Any insight on what I should be rather doing differently?
I am doing it like here: https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/#:~:text=%22MultiWiggleAdapter%22%2C-,%22,-bigWigs%22%3A. But instead of URLs these are bigwig file paths stored locally.
Thank you!

[cmdcolin]

@rshakhb10 this is actually a oversight in the design of the system, you have to refer to absolute URLs when using the bigWigs array currently. if you want to use relative URLs you can use the subadapters array

mentioned here #3430 (comment)

[cmdcolin]

I'll make an issue from this discussion so this has a proper issue to track! thanks for reporting

[rshakhb10]

Hmmm, but it looks like that neither relative or absolute paths work... it only seemed to work when I switched to the subadaptors

[cmdcolin]

what error did you see? just for reference, this is an example of an example of a config using absolute paths

jbrowse-components/test_data/config_demo.json

Lines 3969 to 4001 in d9e5ecc

	{
	"type": "MultiQuantitativeTrack",
	"trackId": "microarray_multi",
	"name": "MultiWig",
	"category": ["ENCODE bigWigs"],
	"assemblyNames": ["hg19"],
	"adapter": {
	"type": "MultiWiggleAdapter",
	"bigWigs": [
	"https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig",
	"https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig",
	"https://www.encodeproject.org/files/ENCFF858LIM/@@download/ENCFF858LIM.bigWig",
	"https://www.encodeproject.org/files/ENCFF425TNW/@@download/ENCFF425TNW.bigWig",
	"https://www.encodeproject.org/files/ENCFF207RBY/@@download/ENCFF207RBY.bigWig",
	"https://www.encodeproject.org/files/ENCFF289CTN/@@download/ENCFF289CTN.bigWig",
	"https://www.encodeproject.org/files/ENCFF884IEG/@@download/ENCFF884IEG.bigWig",
	"https://www.encodeproject.org/files/ENCFF495SBQ/@@download/ENCFF495SBQ.bigWig",
	"https://www.encodeproject.org/files/ENCFF959EZF/@@download/ENCFF959EZF.bigWig",
	"https://www.encodeproject.org/files/ENCFF926YZX/@@download/ENCFF926YZX.bigWig",
	"https://www.encodeproject.org/files/ENCFF269CHA/@@download/ENCFF269CHA.bigWig",
	"https://www.encodeproject.org/files/ENCFF857KTJ/@@download/ENCFF857KTJ.bigWig",
	"https://www.encodeproject.org/files/ENCFF109KCQ/@@download/ENCFF109KCQ.bigWig",
	"https://www.encodeproject.org/files/ENCFF942TZX/@@download/ENCFF942TZX.bigWig",
	"https://www.encodeproject.org/files/ENCFF140HPM/@@download/ENCFF140HPM.bigWig",
	"https://www.encodeproject.org/files/ENCFF305JRR/@@download/ENCFF305JRR.bigWig",
	"https://www.encodeproject.org/files/ENCFF739FDJ/@@download/ENCFF739FDJ.bigWig",
	"https://www.encodeproject.org/files/ENCFF518OJP/@@download/ENCFF518OJP.bigWig",
	"https://www.encodeproject.org/files/ENCFF810HHS/@@download/ENCFF810HHS.bigWig",
	"https://www.encodeproject.org/files/ENCFF939JSB/@@download/ENCFF939JSB.bigWig",
	"https://www.encodeproject.org/files/ENCFF041TAK/@@download/ENCFF041TAK.bigWig"
	]
	}
	},

but if subadapters works, might be best for now anyways since it supports the relative paths

[rshakhb10]

yes I am doing something similar but instead of URLs, I point to the locally stored files like /path/to/the/file/file.bigWig and it doesn't work... is it only intended for urls? It gives a 404 error, file cannot be found

[cmdcolin]

yes, technically everything is a URL to jbrowse. this is basically because jbrowse has no "server side" so it can't access e.g. absolute paths on the file system, only URLs so a URL like /path/to/the/file/file.bigWig would be resolved as http://yourserver.com/path/to/the/file/file.bigWig

[rshakhb10]

okay, yeah it can't fetch it, despite that the file is present...