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-data-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
