hg38 reference genome files unavailable

[Emre Colak]

Hi,

Starting a few hours ago, I am unable to reach the following files:

https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa
https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai

These files used to be public, but I keep getting http 403 now. Have these files been removed or have they been moved under a new authentication scheme?

Best,

Emre Colak

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[igv-help]

All amazon hosts are being decommisioned.   Newer versions of IGV should not be affected, but if you are on an older version you might need to edit your preferences to point to new locations.   What version of IGV are you on?

[Emre Colak]

Thanks for replying.

We're using 2.15.13 and setting it up like in this example https://igv.org/doc/igvjs/#Reference-Genome/#example

What are the new locations for these files that we can point to?

Best,

Emre

[igv-help]

Generally the files are available in github.   This should be the list for 2.15 https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/legacy/genomes.tsv.

Is your "Genome Server URL" custom. (you can see it in "View > Preferences > Advanced")

[Emre Colak]

Not sure, I can't load IGV right now, but thanks a lot for the file locations. I'll give those a try.

Best,

Emre

[igv-help]

If you can't start IGV because of this problem, or even if you can, here is a way to get going.   With IGV shutdown edit the file "prefs.properties" in the IGV folder.  The IGV folder is usually in the user home directory (not not Documents).  Add the following line to prefs.properties then start IGV.   If there is already a line starting with "IGV.genome.sequence.dir" replace it with this.

IGV.genome.sequence.dir=https://igv.org/genomes/genomes.tsv

[Emre Colak]

Thanks, but it sounds these instructions are for the desktop version of IGV, I'm using igv.js

[igv-help]

Ah yes, sorry, for igv.js use the following for your "genomes" property

https://igv.org/genomes/genomes3.json

[Emre Colak]

No worries, thanks for the help.