Hello Hiram, I tried "hideAll=1", but I still got the same error message. (as attached screenshot) I loaded most of the tables by a perl script I wrote. (as attached image) Some tables are loaded by mysql "LOAD DATA" commands. I wish I have a sold IP address so that one of you can login and figure it out more tangibly.
Thanks, Woody 2010/10/28 Hiram Clawson <[email protected]> > Good Morning Woody: > > This is most likely some kind of odd problem in our code. The browser > should > work just fine even with missing tables such as these. Try opening your > hgTracks with the argument: hgt.hideAll=1 added to the URL in your WEB > browser, e.g.: > > http://your.server/cgi-bin/hgTracks?hgt.hideAll=1 > > This will turn off all tracks. > > Can you clarify how you get your trackDb table loaded into your hg19 > database ? > Are you merely copying our copy of that table into your MySQL, or > constructing > it with a 'make alpha' in the trackDb directory ? > > --Hiram > > > Woody Lin wrote: > >> Hello Mary, >> >> Thanks for the reply. I have imported all the tables of hg19 and hgFixed >> into MySQL database, and I do have all minimum set of tables required. >> Accordingly, it could be because of the gbdb files. Based on the steps of >> installation manual on the UCSC genome browser, I don't see how to install >> gbdb files. I do find gbDbLoadStep under one of the folders under kent. >> (see >> attached image) Should I "make install it" and move it to cgi-bin or >> somewhere else? >> >> Thank you. >> Bests, >> Woody >> >> 2010/10/27 Mary Goldman <[email protected]> >> >> Hi Woody, >>> >>> Our best guess is that you are either missing key tables (see below), >>> your >>> trackDb table is not up-to-date or your gbdb files are out of sync with >>> your >>> MySQL tables. We recommend re-downloading the minimum set of tables >>> required >>> for the Genome Browser ( >>> http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation). >>> >>> I hope this information is helpful. Please feel free to contact the mail >>> list again if you require further assistance. >>> >>> Best, >>> Mary >>> ------------------ >>> Mary Goldman >>> UCSC Bioinformatics Group >>> >>> ----- Original Message ----- >>> From: "Woody Lin" <[email protected]> >>> To: [email protected] >>> Sent: Tuesday, October 26, 2010 3:37:54 AM GMT -08:00 US/Canada Pacific >>> Subject: [Genome] Question about installing genome browser (error: >>> wgEncodeGisDnaPet) >>> >>> Dear all, >>> >>> I tried to install genome browser (hg19) on my computer, but I came upon >>> the >>> error message as following and found no solutions on the internet or >>> genome >>> browser mailing list. >>> >>> Parent track wgEncodeGisDnaPet of child wgEncodeGisDnaPetViewAlignments >>> doesn't exist >>> >>> Could someone help me how to deal with the problem? Thank you so much! >>> >>> Bests, >>> Woody >>> >>
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