This previous mailing list thread might also have some useful information: https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-October/002139.html
On 12/16/11 2:39 PM, Greg Roe wrote: > Hi Hongyu, > > We're pretty sure that the error you're getting is Ubuntu specific. > (Googling " ubuntu mysql connect socket" comes up with a lot of hits > with people having this issue.) > > Two things to try... > > Try to set db.socket as suggested here: > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2011-August/002722.html > > > If this does not work, try the "Problem 2" solution in this thread: > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/001949.html > > > Please let us know if you have any additional questions: > [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > On 12/12/11 11:31 PM, Hongyu Zhang wrote: >> Hi Greg, >> >> the value of "socket" is >> >> | socket | /var/run/mysqld/mysqld.sock >> >> Hongyu >> >> 2011/12/13 Greg Roe<[email protected]> >> >>> Hi Hongyu, >>> >>> Can you issue a "show variables;" command and let us know what is the >>> value of "socket" displayed is? >>> >>> For example you may see something like: >>> >>> | socket | /var/lib/mysql/mysql.sock >>> >>> >>> Please reply to:[email protected] >>> - >>> Greg Roe >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> On 12/10/11 12:58 AM, Hongyu Zhang wrote: >>> >>>> Hi, >>>> >>>> I have installed the genome browser on my Ubuntu 11.10, I can access >>>> the mysql in the terminal: >>>> >>>> mysql -ureadwrite -pupdate --socket /var/run/mysqld/mysqld.sock >>>> mysql -ureadonly -paccess --socket /var/run/mysqld/mysqld.sock >>>> mysql -ubrowser -pgenome --socket /var/run/mysqld/mysqld.sock >>>> >>>> But, when I access to the genome browser, the following error occurs: >>>> >>>> Couldn't connect to database (null) on localhost as readwrite. Can't >>>> connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' >>>> (13) >>>> >>>> >>>> The content of hg.conf under cgi-bin list as follow: >>>> >>>> db.host=localhost >>>> db.user=readonly >>>> db.password=access >>>> >>>> db.socket=/var/run/mysqld/**mysqld.sock >>>> db.port=3306 >>>> >>>> defaultGenome=Human >>>> >>>> db.trackDb=trackDb >>>> >>>> db.grp=grp >>>> >>>> wiki.host=genomewiki.ucsc.edu >>>> wiki.userNameCookie=wikidb_**mw1_UserName >>>> wiki.loggedInCookie=wikidb_**mw1_UserID >>>> >>>> customTracks.host=<your specific host name> >>>> customTracks.user=<your specific MySQL user for this function> >>>> customTracks.password=<MySQL password for specified user> >>>> customTracks.useAll=yes >>>> customTracks.tmpdir=/data/tmp/**ct >>>> >>>> browser.indelOptions=on >>>> >>>> central.db=hgcentral >>>> central.host=localhost >>>> >>>> central.user=readwrite >>>> central.password=update >>>> central.domain=mylab.**university.edu<http://mylab.university.edu> >>>> >>>> browser.background=../images/**floret.jpg >>>> >>>> browser.documentRoot=/usr/**local/apache/htdocs >>>> >>>> grepIndex.genbank=/data/tmp/**grepIndex >>>> grepIndex.default=/gbdb >>>> >>>> backupcentral.db=hgcentral >>>> backupcentral.host=localhost >>>> backupcentral.user=readwrite >>>> backupcentral.password=update >>>> >>>> archivecentral.db=hgcentral >>>> archivecentral.host=localhost >>>> archivecentral.user=readwrite >>>> archivecentral.password=update >>>> >>>> hgc.psxyPath=/hive/data/**outside/GMT4.3.1/bin/psxy >>>> hgc.ps2rasterPath=/hive/data/**outside/GMT4.3.1/bin/ps2raster >>>> hgc.ghostscriptPath=/usr/bin/**ghostscript >>>> >>>> Could you please tell me what's the problem? >>>> >>>> Many thanks! >>>> >>>> Hongyu Zhang >>>> Shanghai Cancer Institute >>>> ______________________________**_________________ >>>> Genome-mirror mailing list >>>> [email protected] >>>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome-mirror<https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror> >>>> >> _______________________________________________ >> Genome maillist [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
