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 <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
