Hi Brad,

I just ran the updateucsc.sh script and it seemed to work correctly. Can you be more specific as to which builds you are missing and could you try running the script again and if it doesn't work, copy the log output here?

Thanks for using Galaxy,

Dan

On Mar 6, 2012, at 12:15 PM, Langhorst, Brad wrote:

It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone...

Has anybody else observed this? Fixed it?

Brad

Brad Langhorst langhorst@neb.com 978-380-7564

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Hello,

Yes, this was noticed but it took a few days to track down and correct the problem. As of this afternoon, the genome builds list was restored to the original content plus a few new additions.

If you notice any genome missing that was previously present, we would definitely like to know.

Very sorry for the inconvenience!

Best,

Jen Galaxy team

On 3/6/12 2:14 PM, Langhorst, Brad wrote:

Hi Dan:

When I look at builds.txt I see only the eukaryotic genomes...

the canary that triggered my investigation was eschColi_K12.

It used to be present, but is now not in builds.txt it is present in ucsc_build_sites.txt

When i go to the xml at ucsc's test server http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn i don't see eschColi_K12

I've looked in my backups and I find that the builds.txt from 3 weeks ago did have eschColi_K12 (and many other now missing items).

I think we'll have to fetch these from the other sites now...

Brad

On Mar 6, 2012, at 4:59 PM, Daniel Blankenberg wrote:

...

Hi Brad,

I just ran the updateucsc.sh script and it seemed to work correctly. Can you be more specific as to which builds you are missing and could you try running the script again and if it doesn't work, copy the log output here?

Thanks for using Galaxy,

Dan

On Mar 6, 2012, at 12:15 PM, Langhorst, Brad wrote:

...

It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone...

Has anybody else observed this? Fixed it?

Brad

Brad Langhorst langhorst@neb.com mailto:langhorst@neb.com 978-380-7564

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-- Brad Langhorst langhorst@neb.com mailto:langhorst@neb.com 978-380-7564

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