Comments (9)
jrobinso
commented on August 16, 2024
As a first step let's ignore the container hierarchy ("componentTrack", "supertrack", etc) and just parse out the track records as a flat list of json objects.
Example track record for a bigBed:
track ENCFF000CBW
type bigBed
bigDataUrl /files/ENCFF000CBW/@@download/ENCFF000CBW.broadPeak.bigbed?proxy=true
parent ENCSR000AUTPKView on
shortLabel ENCFF000CBW
longLabel ChIP-seq of K562 - ENCSR000AUT - ENCFF000CBW broadPeak peaks pooled
visibility pack
subGroups view=PK
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swingingsimian
commented on August 16, 2024
Hi,
Has this dropped from the development path completely? Trackhub support in IGV would be great, especially if it supported authentication for private hubs.
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jrobinso
commented on August 16, 2024
Nothing that is still open has been dropped completely. I am not an
expert on track hubs, do you know how authentication is done?
…On Tue, Apr 11, 2017 at 5:11 AM, Nathan Johnson ***@***.***> wrote:
Hi,
Has this dropped from the development path completely? Trackhub support in
IGV would be great, especially if it supported authentication for private
hubs.
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swingingsimian
commented on August 16, 2024
At present I believe it is basic url user/pw auth, e.g.:
https://user:[email protected]/file
Not well documented, but mentioned here:
https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/GrXgW24IDMA
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Parul-Kudtarkar
commented on August 16, 2024
Hi any updates to support data hubs
i.e.
https://igv.org/web/test/examples/igvjs.html?genome=hg19&hub=https://www.t2depigenome.org/browser_hub/type,,Experiment|assay_title=ATAC-seq/GRCh37/trackDb.json
Thanks!
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jrobinso
commented on August 16, 2024
No but periodic pinging is the secret. Thanks for the example, what would
you expect should happen with such a url?
…On Fri, Apr 5, 2019 at 1:46 PM Parul Kudtarkar ***@***.***> wrote:
Hi any updates to support data hubs
i.e.
https://igv.org/web/test/examples/igvjs.html?genome=hg19&hub=https://www.t2depigenome.org/browser_hub/type,,Experiment|assay_title=ATAC-seq/GRCh37/trackDb.json
Thanks!
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jrobinso
commented on August 16, 2024
Let me expand on my question, do you expect all the tracks in the json to
be loaded, or for a selection menu of some type to be created from the
tracks?
On Fri, Apr 5, 2019 at 2:22 PM James Robinson <[email protected]>
wrote:
… No but periodic pinging is the secret. Thanks for the example, what
would you expect should happen with such a url?
On Fri, Apr 5, 2019 at 1:46 PM Parul Kudtarkar ***@***.***>
wrote:
> Hi any updates to support data hubs
> i.e.
>
> https://igv.org/web/test/examples/igvjs.html?genome=hg19&hub=https://www.t2depigenome.org/browser_hub/type,,Experiment|assay_title=ATAC-seq/GRCh37/trackDb.json
>
> Thanks!
>
> —
> You are receiving this because you modified the open/close state.
> Reply to this email directly, view it on GitHub
> <#46 (comment)>, or mute
> the thread
> <https://github.com/notifications/unsubscribe-auth/AA49HPE20EEHeqV1VZUL91bwSA0RxEvsks5vd7YigaJpZM4DwvSB>
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>
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Parul-Kudtarkar
commented on August 16, 2024
@jrobinso I would set a limit for example view up to 50 tracks, based on selection menu. the classic example is UCSC genome browser track hubs - http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt
I am hoping for something on similar lines with embed-able browser
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jrobinso
commented on August 16, 2024
Right, but I think the right thing to do is create a selection menu as UCSC
does. In this view the right place for track hubs is igv-webapp, not
igv.js. igv.js is just the visualization component, it does not supply
load menus, etc. Its a component for building web apps, its not a webapp
by itself.
I will give this some thought, but I think trackhubs should be supported by the containing app, not the viz component. The UCSC page you reference is analogous to igv-webapp, the
top half === igv.js, the track selection stuff is === igv-webapps track
load menus.
What is the hosting app for your instance of igv.js?
…On Fri, Apr 5, 2019 at 4:59 PM Parul Kudtarkar ***@***.***> wrote:
@jrobinso <https://github.com/jrobinso> I would set a limit for example
view up to 50 tracks, based on selection menu. the classic example is UCSC
genome browser track hubs -
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt
I am hoping for something on similar lines with embed-able browser
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Related Issues (20)
- The YC tag in bam does not work and does not display the corresponding color HOT 5
- Docs: Add `compressedIndexURL` and clarify `indexURL` behavior HOT 5
- copy sequence from selected region as in IGV desktop HOT 2
- Issue with Loading Large GWAS Data Track in igv.js HOT 6
- IGV renames "chromosome_1" to "omosome_1" HOT 3
- Inquiry About Highlighting SNPs in IGV.js HOT 16
- Add option to display alignments arranged 1 per line
- customize a reference genome
- loadTracks example not working HOT 2
- Make igv.js work with TypeScript: Add TypeScript API description HOT 8
- a lot of tracks are blank at first and only appear when you change the locus. HOT 3
- Sequence Track not using nucleotideColors creation option HOT 2
- IGV in a secondary tab does not show initially HOT 5
- Alignment coverage track base mismatch depth indicator missing HOT 3
- Baseline shift for spliceJunction tracks? HOT 5
- Issue with searching consecutive regions with .search() in same IGV browser since v3.0.0 HOT 3
- ERROR: Cannot read properties of undefined (reading 'table') HOT 5
- VariantTrack header.INFO undefined HOT 1
- Htsget Bam support broken since v2.9.0 HOT 7
- IGVweb not loading GFF compressed and index files when served from a server HOT 13
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