You need to update tables and /gbdb/ files at the same time. They do not want to be out of synchronization with each other.
Use rsync to update your table and files, just like you used rsync to first fetch the data. --Hiram WANG Wuqi wrote: > Hi Hiram, > > Thanks a lot. > > Is it from rsync://hgdownload.cse.ucsc.edu/mysql/hg18/ for tables > updating? > this means overwrite our all current mysql tables. > > > Best & Regards > > Wuqi > > > > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Wednesday, April 08, 2009 2:16 PM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: Search errors in GBrowser > > You use the rsync command to fetch new data to update your > gbdb and mysql tables. For example > > # cd /gbdb/hg18 > # rsync -azP --stats rsync://hgdownload.cse.ucsc.edu/gbdb/hg18/ ./ > > Same idea for your mysql tables. > > Beware if you use the --delete option in case you have local > data in your system. That would delete your local data. > > --Hiram > > WANG Wuqi wrote: >> Hi Hiram, >> >> What organism genome assembly are you using ? >> -- Human, mouse, zebrafish and medaka. >> >> The item 'uc001acj.1' can be searched in http://genome.ucsc.edu/. >> >> We use a private genome browser, how to update our tables and /gbdb/ ? >> >> >> Thanks & Regards >> >> Wuqi >> >> >> >> -----Original Message----- >> From: Hiram Clawson [mailto:[email protected]] >> Sent: Tuesday, April 07, 2009 9:44 PM >> To: WANG Wuqi >> Cc: [email protected] >> Subject: Re: Search errors in GBrowser >> >> What genome browser WEB site are you using ? >> >> What organism genome assembly are you using ? >> >> Both of your example searches appear to work just >> fine at http://genome.ucsc.edu/ >> >> If this is your private genome browser, perhaps >> your tables and /gbdb/ files need an update ? >> >> --Hiram >> >> WANG Wuqi wrote: >>> >>> >>> Hi Hiram, >>> >>> >>> >>> In Gbrowser, to encounter below errors when search 'uc001acj.1': >>> >>> >>> >>> Sorry, couldn't locate uc001acj.1 in genome database >>> >>> >>> >>> But when try to search 'uc001aab.1', it is ok. >>> >>> >>> >>> i.e. some search can be done, some can not. >>> >>> >>> >>> >>> >>> And, when I search 'uc001acj.1', in MYSQL trace log file to find >> below >>> Mysql statements: >>> >>> ----------------------. >>> >>> 14553 Connect reado...@localhost on hg18 >>> >>> 14553 Quit >>> >>> 14552 Query select chrom,chromStart,chromEnd,name >>> >>> from DHP001fr_hg18_07032008_A_v1 where name like >>> '%uc001acj.1%' >>> >>> 14554 Connect reado...@localhost on hg18 >>> >>> 14554 Quit >>> >>> 14552 Query select name,chrom,txStart,txEnd from knownGene >>> >>> where name in ("uc001acj.2") >>> >>> 14552 Query select kgID,geneSymbol,description >>> >>> from kgXref where kgID in ("uc001acj.2") >>> >>> 14555 Connect reado...@localhost on hg18 >>> >>> 14555 Quit >>> >>> 14552 Query select chrom,chromStart,chromEnd,name from >> switchDbTss >>> where name like 'uc001acj.1%' >>> >>> ----------------------. >>> >>> >>> >>> It is strange, I search "uc001acj.1", but see "uc001acj.2" in sql. >>> >>> >>> >>> >>> >>> Please help >>> >>> >>> >>> >>> >>> Thanks & Regards >>> >>> >>> >>> Wuqi >>> >>> >>> >>> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
