Hello, You are correct, the variable for organism in the labels are not being interpreted correctly during the make process.
The browser source code has been updated to mySQL version 5 since the code base release v214. Many adjustments were made to utilities to support the change. Genomic assemblies were updated incrementally, but all are converted now. The programs in the source code that were altered are listed in a posting to the genome-mirror mailing list at each release. https://lists.soe.ucsc.edu/pipermail/genome-mirror/ https://lists.soe.ucsc.edu/pipermail/genome-mirror/2009-September/001412.html https://lists.soe.ucsc.edu/pipermail/genome-mirror/2009-September/001413.html You have two options: either roll back to v213 or update to mySQL version 5. Using a mixed set (make Alpha from v213 and other utilities from v214 or later) is possible, but not recommended. It is difficult to predict what other issues would pop up. But you can always try it out and see what happens. You may be interested in subscribing to the genome-mirror mailing list. It is fairly low-volume. A digest version would help you to know when a source code update has been released and what changed. Occasionally major data changes are also posted, very useful if you perform regular updates, as some of these involve warning about the release of very large or altered datasets. We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "WANG Wuqi" <[email protected]> wrote: > From: "WANG Wuqi" <[email protected]> > To: "Hiram Clawson" <[email protected]> > Cc: "WANG Wuqi" <[email protected]>, [email protected] > Sent: Tuesday, November 24, 2009 2:11:20 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Track name prefix $o > > Hi Hiram, > > Our genome browser mirror site version is v219, MySQL is version 4.0. > > We find a number of track name prefix "$o" in group " Comparative > Genomics" of hg18(Please see attachment). Also we do not find > corresponding entry in file trackDb.ra, so I update the 'shortLabel' > and 'longLabel' in the table hg18.trackDb depending on latest table > hg18.trackDb > Information, the track names are changed too in gonome browser and do > not appear track name with prefix "$o", but when I do "make alpha > DBS=hg18", the track names come repristination. > > Please give advice > > Thanks & regards > > Wuqi > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
