New UMD builds of jbrowse-linear-genome-view embeddable component

[ZWanBing]

hello ! I have used the plugin jbrowse2 with s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-view/[email protected]/umd/jbrowse-linear-view.js
And I noticed that the main release of jbrowse2 can support better indel indications , so could I use this function in the plugin website by a newer js file? Thanks a lot♥

[ZWanBing]

#1890 (comment)
I have used the plugin to make a linear genome viewer on my server so our teammates can view mutation sites with a link directed to a html file with set bam and chromosome position. But the plugin js file is an old version of jbrowse2, so could you provide the recent version of this js script s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-view/[email protected]/umd/jbrowse-linear-view.js? We have urgent needs to get better view on indel.
Thank you so much!

[garrettjstevens]

Hi @ZWanBing,

We don't have automated builds yet of the UMD build of our embeddable linear genome view. You can watch this issue for updates on that: #1028. I have gone ahead and done a manual build, though, based off the latest v1.0.0 release. You can access it at:

http://s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-genome-view/jbrowse-linear-genome-view%40v1.1.0/umd/jbrowse-linear-genome-view.js

Note that there has been a change since the version you have been using, and to create the view you will need to use new JBrowseLinearGenomeView() (previously it was new JBrowseLinearView()).

Also note that this build is a small wrapper around our linear genome view React component @jbrowse/react-linear-genome-vew, which is released regularly, so if it suits your needs you can use that as well.

[ZWanBing]

Thanks a lot! I have test it but with the defaultsession it does not work. Below is the website use this plugin:

<script src="//s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-genome-view/[email protected]/umd/jbrowse-linear-genome-view.js"></script>

Test

<script type="module"> import assembly from './assembly.js' import tracks from './tracks.js' const genomeView = new JBrowseLinearGenomeView({ container: document.getElementById('jbrowse_linear_view'), assembly, tracks, location: 'chr15:66729068', defaultSession:{ name:"defaultSession", view:{ "id": "linearGenomeView", "type": "LinearGenomeView", "offsetPx": 5608767607, "bpPerPx": 0.02, "displayedRegions": [{ "refName": "chr5", "start": 0, "end": 180915260, "reversed": false, "assemblyName": "hg19" }], "tracks": [{ "id": "ReferenceSequence", "type": "ReferenceSequenceTrack", "height": 100, "configuration": "hg19-ReferenceSequenceTrack" }, { "id": "x-j__C_nM", "type": "AlignmentsTrack", "height": 97, "configuration": "2000191.recal-H", "PileupTrack": { "id": "mrQcOy181Q", "type": "PileupTrack", "height": 100, "configuration": { "type": "PileupTrack", "trackId": "2000191.recal-H_pileup_xyz", "name": "2000191 pileup", "assemblyNames": [ "hg19" ], "category": [ "tumor" ], "adapter": { "type": "BamAdapter", "bamLocation": { "uri": "2000191.recal-H.bam" }, "index": { "location": { "uri": "2000191.recal-H.bai" } }, "sequenceAdapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "hg19.fasta" }, "faiLocation": { "uri": "hg19.fasta.fai" } } }, "renderers": { "PileupRenderer": { "type": "PileupRenderer" }, "SvgFeatureRenderer": { "type": "SvgFeatureRenderer" } } } }, "SNPCoverageTrack": { "id": "DvhupI7m-T", "type": "SNPCoverageTrack", "height": 40, "configuration": { "type": "SNPCoverageTrack", "trackId": "2000191.recal-H_snpcoverage_xyz", "name": "2000191 snpcoverage", "assemblyNames": [ "hg19" ], "category": [ "tumor" ], "adapter": { "type": "SNPCoverageAdapter", "subadapter": { "type": "BamAdapter", "bamLocation": { "uri": "2000191.recal-H.bam" }, "index": { "location": { "uri": "2000191.recal-H.bai" } }, "sequenceAdapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "hg19.fasta" }, "faiLocation": { "uri": "hg19.fasta.fai" } } } }, "renderers": { "SNPCoverageRenderer": { "type": "SNPCoverageRenderer" } } }, "selectedRendering": "" }, "showCoverage": true, "showPileup": true }, { "id": "EcMTHWIop", "type": "AlignmentsTrack", "height": 240, "configuration": "2000192.recal-H", "PileupTrack": { "id": "wIZAEuVjB4", "type": "PileupTrack", "height": 100, "configuration": { "type": "PileupTrack", "trackId": "2000192.recal-H_pileup_xyz", "name": "2000192 pileup", "assemblyNames": [ "hg19" ], "category": [ "normal" ], "adapter": { "type": "BamAdapter", "bamLocation": { "uri": "2000192.recal-H.bam" }, "index": { "location": { "uri": "2000192.recal-H.bai" } }, "sequenceAdapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "hg19.fasta" }, "faiLocation": { "uri": "hg19.fasta.fai" } } }, "renderers": { "PileupRenderer": { "type": "PileupRenderer" }, "SvgFeatureRenderer": { "type": "SvgFeatureRenderer" } } } }, "SNPCoverageTrack": { "id": "u8_9Ka-4C7", "type": "SNPCoverageTrack", "height": 40, "configuration": { "type": "SNPCoverageTrack", "trackId": "2000192.recal-H_snpcoverage_xyz", "name": "2000192 snpcoverage", "assemblyNames": [ "hg19" ], "category": [ "normal" ], "adapter": { "type": "SNPCoverageAdapter", "subadapter": { "type": "BamAdapter", "bamLocation": { "uri": "2000192.recal-H.bam" }, "index": { "location": { "uri": "2000192.recal-H.bai" } }, "sequenceAdapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "hg19.fasta" }, "faiLocation": { "uri": "hg19.fasta.fai" } } } }, "renderers": { "SNPCoverageRenderer": { "type": "SNPCoverageRenderer" } } }, "selectedRendering": "" }, "showCoverage": true, "showPileup": true } ], "hideHeader": false, "hideHeaderOverview": false, "trackSelectorType": "hierarchical", "showTrackLabels": true, "showCenterLine": true }} }) </script>

What could I do to fix this?

[garrettjstevens]

Hi @ZWanBing,

Sorry I didn't see your problem before. It looks like you edited your original comment and replaced it with that message. Just so you know, I don't get email notifications when a comment is edited, so it's probably best to make a new comment instead to make sure I see them.

What problem are you getting when you try to load that defaultSession? I'd probably try re-creating the defaultSession, perhaps using a method like is described here: https://jbrowse.org/jb2/docs/bcc2020_embedding_jbrowse_08_default_session

[garrettjstevens]

There's a new manual beta build based on the latest release at:

https://s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-genome-view/jbrowse-linear-genome-view%40v1.3.2/umd/jbrowse-linear-genome-view.js

[garrettjstevens]

UMD builds are now officially released starting with v1.3.5. The interface has changed slightly since the beta version from our previous tutorial, and you can see the new tutorial here.

You can also browse the available build files on UNPKG.