npm installation fails about igv-ui

[jrobinso]

igv-ui is not an NPM module, it is a component for the igv.js project and not designed to be used stand-alone. What are you hoping to do with it?

[adadiehl]

Encountered this error trying to install igv via 'node install igv' -- attempted node install from the igv-ui git repository when this failed. Posted the error here because the issue is directly with igv-ui installation, not igv installation.

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-A

On Tue, Jun 15, 2021 at 11:33 AM Jim Robinson ***@***.***> wrote: igv-ui is not an NPM module, it is a component for the igv.js project and not designed to be used stand-alone. What are you hoping to do with it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSLLOVGGJEBYRUXXNT3TS5XDJANCNFSM46XOEELQ> .

[jrobinso]

I don't know what "node install" does. 'npm install igv' works for me.

[adadiehl]

Sorry, npm install

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On Tue, Jun 15, 2021 at 12:00 PM Jim Robinson ***@***.***> wrote: I don't know what "node install" does. 'npm install igv' works for me. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSMEC6LBWGZBRBSC2TLTS52LRANCNFSM46XOEELQ> .

[adadiehl]

Based on the error message, seems to be a permissions issue. Likely works for you because you have dev permissions on the repository. Original error message appeared to have some potentially useful information to resolve the problem.

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On Tue, Jun 15, 2021 at 12:06 PM Adam Diehl ***@***.***> wrote: Sorry, npm install On Tue, Jun 15, 2021 at 12:00 PM Jim Robinson ***@***.***> wrote: > I don't know what "node install" does. 'npm install igv' works for me. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#41 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/ACUMZSMEC6LBWGZBRBSC2TLTS52LRANCNFSM46XOEELQ> > . >

[jrobinso]

It runs on every commit via github workflow, and we have ~4,000 NPM installs weekly from organizations other than ourselves.

[jrobinso]

So its a puzzle.

[adadiehl]

Indeed. Good news is I managed to work around the issue by linking directly to the codebase in my index.html. Guess it's going to be included on all pages instead of just where it's needed. Oh well...

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On Tue, Jun 15, 2021 at 12:11 PM Jim Robinson ***@***.***> wrote: So its a puzzle. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSOUTODZZI3UOGTAMPDTS53TPANCNFSM46XOEELQ> .

[jrobinso]

I have also had weird errors installing packages from github. I have on my to-do list just to put these dependent projects in NPM, I think that will solve this sort of error permanently. This one is especially strange as we are both on the same node and NPM versions. You might track clearing your NPM cache.

[adadiehl]

Unfortunately, clearing the npm cache didn't do the trick. Based on what you're saying, I'm probably a weird edge case. However, I was able to get around it by linking to the scripts, so I'm good to go -- well, almost... That said, since I have you on the line, so to speak, I hope you don't mind if I run another issue past you. This one seems likely to be an issue with my implementation, not the igv.js code base, so probably not appropriate to open a new issue! I'm putting together a tool for viewing aligned plasmid sequences, where the reference is a fasta file describing the plasmid sequence and the single track is the bam file of reads aligned to the plasmid file. Fasta references and bam files are stored in a tmp folder on our server and retrieved with an api call. I've verified the api calls are returning the correct files, but am hitting a brick wall when I try to load a reference into a new igv.js instance. Looks as if the chromosome names are not being parsed out when the fasta file is loaded, but I can't quite tell why based on the igv.js code. Attaching a representative fasta file, code for invoking the igv session, and the stack trace. I've also tried indexing with faidx and including the indexURL param in the reference block and am getting similar errors. Hoping you can spot the problem and point me in the right direction. Thank you for all your help! Best Regards, Adam Diehl class ResultsDisplay extends Component { // initialize our state constructor(props) { super(props); this.state = { serverId: 7573260109, refFile: "dp104_p4_2xSymmetricLacO_0_reference.fasta", algnFile: "filtered_alignment.bam" }; } componentDidMount() { const igvDiv = document.getElementById("igv-div"); let options = { reference: { "name": this.state.refFile, "fastaURL": browser.apiAddr + '/getResult?serverId=' + this.state.serverId + "&fileName=" + this.state.refFile, "indexed": false }, tracks: [ { "name": "Alignment", "url": browser.apiAddr + '/getResult?serverId=' + this.state.serverId + "&fileName=" + this.state.algnFile, "format": "bam" } ] }; igv.createBrowser(igvDiv, options) .then(function (browser) { console.log("Created IGV browser"); }); } componentWillUnmount() { // Clean up our area. } // Render the UI. render() { return ( <div id="igv-div"> </div> ); } } Uncaught (in promise) TypeError: Cannot read property 'startsWith' of undefined at genome.js:172 at Array.forEach (<anonymous>) at new Uo (genome.js:171) at Object.loadGenome (genome.js:57) at async Hu.loadReference (browser.js:607) at async Hu.loadSessionObject (browser.js:501) at async Object.createBrowser (igv-create.js:74)

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On Tue, Jun 15, 2021 at 12:48 PM Jim Robinson ***@***.***> wrote: I have also had weird errors installing packages from github. I have on my to-do list just to put these dependent projects in NPM, I think that will solve this sort of error permanently. This one is especially strange as we are both on the same node and NPM versions. You might track clearing your NPM cache. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSKED7NUCWY373RTSQDTS577HANCNFSM46XOEELQ> .

[jrobinso]

Most likely, this is not returning what you think it is. I have no way to verify that of course. Try pasting that URL into a web browser and see what's returned.

browser.apiAddr + '/getResult?serverId=' + this.state.serverId + "&fileName=" + this.state.refFile,

[jrobinso]

A more direct test is to observe the network traffic using your browsers developement tools. The response should be the content of the fasta file.

[adadiehl]

You were correct: my function was returning json instead of just the fasta file. It's working now with that resolved. Thank you again for your help! Adam

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On Tue, Jun 15, 2021 at 4:45 PM Jim Robinson ***@***.***> wrote: Closed #41 <#41>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSL2Z7LRHP2IFEC5VP3TS63VXANCNFSM46XOEELQ> .

[Al-Mclean]

Hi @adadiehl, I'm having the same issue to your original post with a different install (homebridge-broadlink-rm plug-in) - could you provide a bit more detail on how you worked around the issue?

Thanks,

Al

[adadiehl]

Hi Al, I was unable to resolve the issue with npm and ended up linking to the source code directly within index.html for the app I'm developing, as described on the github README (https://github.com/igvteam/igv.js). Hope this helps! Best, Adam Diehl

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On Sat, Jul 31, 2021 at 1:49 AM Al-Mclean ***@***.***> wrote: Hi @adadiehl <https://github.com/adadiehl>, I'm having the same issue to your original post with a different install (homebridge-broadlink-rm plug-in) - could you provide a bit more detail on how you worked around the issue? Thanks, Al — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSI2PUICJF3TZY7MBMDT2OFFZANCNFSM46XOEELQ> .

[jrobinso]

I've never been able to reproduce the original problem. npm install igv works beautifully for me. This particular project (igv-ui) is not an npm module, and really not designed for general use outside of the igv projects but if it works for you great.

[adadiehl]

As mentioned before, the issue crops up in the course of a normal npm install of igv.js. The cause of that failure traced to the failure to install igv-ui as a dependency. The attempts to install igv-ui as a standalone were solely meant to address this issue, since, in my experience, installing the underlying (failed) dependencies often fixes npm install problems. This is not the case for igv-ui, unfortunately. I am sorry if the original issue submission was unclear in this regard. That said, linking to the code works beautifully. Just be aware that installation of the whole package will fail as a result of this limitation in some (likely isolated) cases. It may be worth adding a warning somewhere in the installation docs with a recommendation to link to the source code in cases of installation failure. This might save us all some time in future. Cheers, Adam Diehl

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On Mon, Aug 2, 2021 at 1:43 PM Jim Robinson ***@***.***> wrote: I've never been able to reproduce the original problem. npm install igv works beautifully for me. This particular project (igv-ui) is not an npm module, and really not designed for general use outside of the igv projects but if it works for you great. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACUMZSJJEG6R5TKFP342PEDT23KLVANCNFSM46XOEELQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[jrobinso]

@adadiehl If I knew what the "isolated cases" were I could add a warning, but more likely I would fix them. We have automated builds, on multiple platforms, and something on the order of 10,000 installations, so whatever causes this is rare.

[jrobinso]

A key question here is why is your build system trying to install igv-ui in the first place? Its not part of the igv.js distribution, all required packages are rolled up in igv.esm.js.

[jrobinso]

OK I don't know why you can't install igv-ui, perhaps your build or package manager can't install from github or there is some issue with our configuration, but the project is not needed at runtime so I moved the dependency to "dev-dependencies", which is probably where it belongs anyway. This might fix the problem, certainly it should prevent attempts to install igv-ui from an "igv" install.