Auto-update stale genomes -- Was "RefGet track doesn't migrate to new endpoints on newer versions?"

[brainstorm]

Hello Jim,

One of our cancer curators noticed that her RefGet IGV track was gone, she had this configuration under $HOME/igv/genomes/hg38.json:

I compared with mine and I had these (working) endpoints instead:

% cat igv/genomes/hg38.json
{
  "id": "hg38",
  "name": "Human (hg38)",
  "fastaURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
  "indexURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
  "cytobandURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",
  "tracks": [
    {
      "name": "Refseq Genes",
      "format": "refgene",
      "url": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg38/ncbiRefGene.txt.gz",
      "indexed": false,
      "visibilityWindow": -1,
      "removable": false,
      "order": 1000000
    }
  ]
}

We ended up fixing it by simply running rm -rf $HOME/igv/genomes and restarting IGV.

Would it make sense to add some extra warning/messaging to the user or directly replace those S3 urls on disk if old non-working ones are detected?

Cheers!

[jrobinso]

Thanks for the report, the removal of that file was not intentional. I will restore it for backward compatibility. We do not currently remove files we think are being used. The time will come when we have to do that, but have not done so yet (intentionally). There is a general problem of "stale" genome json files in users "igv" directories. This is partly intentional, I don't like disturbing users setups without explicit action on their part. But it is a problem, we might need to add an opt-in auto-update or other messaging. We are slowly migrating all our amazon hosted files to UCSC hosted equivalents. In the meantime users can always update to the latest genome json by re-downloading it from the "Genomes" menu. Leave this issue open as a reminder to self to deal with the issue of stale genome files. I am also going to restore the missing files. < UPDATE: restored>

…

-- Jim