genome 'hg19' is not currently supported

[heimannch]

Hi Paul,

My app is getting this error whenever igv is loading:

[1] --- leaving igvShiny.R, renderIgvShiny
Warning: Error in igvShiny::parseAndValidateGenomeSpec: Your genome 'hg19' is not currently supported
Currently supported: 
  99: stop
  98: igvShiny::parseAndValidateGenomeSpec
  97: ::
htmlwidgets
shinyRenderWidget [/Users/heimann/Documents/cri_iatlas/iatlas-app/R/germline_gwas_server.R#64]

It's important to us to use this genome version, as our app is mirroring a publication that used this assembly. Is there a reason to stop supporting this version?

Thanks!

[paul-shannon]

Hi Carol,

I think I fixed that a few weeks ago, in igvShiny and igvR. The fix is in

igvShiny/R/genomeSpec.R:

On Mar 16, 2023, at 1:12 PM, Carolina Heimann @.***> wrote:

Hi Paul,

My app is getting this error whenever igv is loading:

[1] --- leaving igvShiny.R, renderIgvShiny Warning: Error in igvShiny::parseAndValidateGenomeSpec: Your genome 'hg19' is not currently supported Currently supported: 99: stop 98: igvShiny::parseAndValidateGenomeSpec 97: :: htmlwidgets shinyRenderWidget [/Users/heimann/Documents/cri_iatlas/iatlas-app/R/germline_gwas_server.R#64]

It's important to us to use this genome version, as our app is mirroring a publication that used this assembly. Is there a reason to stop supporting this version?

Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[paul-shannon]

This is igvShiny version 1.5.9009 from 2023-02-21

On Mar 16, 2023, at 1:12 PM, Carolina Heimann @.***> wrote:

Hi Paul,

My app is getting this error whenever igv is loading:

[1] --- leaving igvShiny.R, renderIgvShiny Warning: Error in igvShiny::parseAndValidateGenomeSpec: Your genome 'hg19' is not currently supported Currently supported: 99: stop 98: igvShiny::parseAndValidateGenomeSpec 97: :: htmlwidgets shinyRenderWidget [/Users/heimann/Documents/cri_iatlas/iatlas-app/R/germline_gwas_server.R#64]

It's important to us to use this genome version, as our app is mirroring a publication that used this assembly. Is there a reason to stop supporting this version?

Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[paul-shannon]

here's the screenshot which failed:

[heimannch]

Thanks for the promptly reply - up and running again!