Thanks to all of you for your prompt responses and suggestions. It's looking as though we're going to create a local mirror of the UCSC database for our use this quarter.
Martin. > -----Original Message----- > From: Maximilian Haussler [mailto:[email protected]] > Sent: Tuesday, April 05, 2011 2:41 PM > To: Hiram Clawson > Cc: Martin Tompa; [email protected] > Subject: Re: [Genome] possibly excessive MySQL queries > > Hi Martin, > > we've had a similar question on Biostar recently and the > person finally found it easier to mirror the UCSC mysql > database than to bother with remote access. If you already > have a mysql server running somewhere, mirroring the ucsc > database for e.g. hg18 requires only one single rsync command. > > Given that you don't want to risk that the mysql access to > ucsc directly gets blocked during the course or just 2 hours > before they have to hand in their exercises (which is likely, > because they will all start 2 hours before the deadline :-), > the best solution could be a local mirror of the database > (not the genome browser website, only the mysql database itself). > > The biostar thread contains the required command: > http://biostar.stackexchange.com/questions/4552/getting-ucsc-d > ata-via-mysql/4554#4554 > > hope this helps > cheers > Max > -- > Maximilian Haussler > Office:+44 161 27 55980 Mob: +44 7574 246 789 > http://www.manchester.ac.uk/research/maximilian.haussler/ > > > > > On Tue, Apr 5, 2011 at 10:51 PM, Hiram Clawson > <[email protected]> wrote: > > > > You could also use the sql definition text files from hgdownload. > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/*.sql > > > > also available via FTP and rsync. > > > > You could rsync all of these .sql files to a local > directory and allow > > everyone to use local files. > > > > If you want to run MySQL exercises, you should use small > samples from > > small tables. Running exercises over an entire database is > an immense > > amount of work. There are several hundred Gb of data in hg19. > > > > --Hiram > > > > ----- Original Message ----- > > From: "robert kuhn" <[email protected]> > > To: "Martin Tompa" <[email protected]> > > Cc: "[email protected]" <[email protected]> > > Sent: Tuesday, April 5, 2011 1:43:02 PM > > Subject: Re: [Genome] possibly excessive MySQL queries > > > > Hi, Martin, > > > > thanks for asking. That might add up to an awful lot of queries if > > you are using a human assembly. there are 1000s of tables in there. > > You might consider parsing the trackDb table first, because the > > entries _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
