Genomic fasta indexes undergoing updates at usegalaxy.org

[jennaj]

Workaround for end-users

1. Wait for this issue to close, then rerun your job(s) at usegalaxy.org
2. Consider working at usegalaxy.eu or usegalaxy.org.au
3. It is fine to have one account at each of these three servers
4. Discussion at Galaxy Help https://help.galaxyproject.org/t/some-tools-have-disconnected-genome-indexes-post-server-updates-open-issue-usegalaxy-org/4629/6?u=jennaj

As of October 20th, 2020 at 7pm EST the issue is still pending a resolution. We expect this to be fixed within the next day, possibly overnight.

Impacted tools can vary. If the tool makes use of a built-in genomic index, it is likely impacted. Some jobs may run Ok and others not. This is primarily due to how jobs are sorted to our clusters, but also related to which tool parameters are invoked.

Examples include...

BamLeftAlign
GetBedFasta
Freebayes
BWA-MEM or any other mapping tool

Test history: https://usegalaxy.org/u/jen-galaxyproject/h/test-bedtools-indexes

[jennaj]

thanks & closing