Dear Hiram, Thanks for your quick response. I will create a new folder called "visiGene" and do the following
rsync -a -P rsync://hgdownload.cse.ucsc.edu/mysql/visiGene/ /home/mysql/mysql/visiGene/ After the files copy, do I need to restart mysql before I use the link from genomebrowser's homepage? By the way, do I need any username/passwd to copy your remote files? Best Wishes, Yan ________________________________________ From: Hiram Clawson [[email protected]] Sent: Wednesday, May 04, 2011 2:24 PM To: Luo, Yan (NIH/NHLBI) [C] Cc: [email protected] Subject: Re: [Genome] Fail to use "visiGene" Pardon me, my pathnames were just examples. Your specific instance appears to be the destination: /home/mysql/mysql/visiGene/ This is a database, it goes in the same directory as all the other databases. Your directory /home/mysql/mysql/ appears to be where your MySQL is keeping all of its databases. --Hiram Luo, Yan (NIH/NHLBI) [C] wrote: > Dear Hiram, > > Thanks for your response. I checked my server of sql account and found the > following folders. > > tninja@junlab-webserver:/home/mysql/mysql$ ls > > debian-5.1.flag hgcentral phpmyadmin sacCer2 > dm3 hgFixed proteins040315 sp040315 > gbrowse_pombe ibdata1 proteins050415 sp050415 > gbrowse_rat ib_logfile0 proteins051015 sp051015 > gbrowse_tair8 ib_logfile1 proteins060115 sp060115 > gnomex junlab-webserver.pid proteins070202 sp070202 > go080130 mm9 proteins080707 sp080707 > hg18 mysql proteins090821 sp090821 > hg19 mysql_upgrade_info rn4 widgets > > > ------ > tninja@junlab-webserver:/home/mysql$ cd mysql > tninja@junlab-webserver:/home/mysql/mysql$ls > > > columns_priv.frm help_relation.MYI slow_log.CSV > columns_priv.MYD help_topic.frm slow_log.frm > columns_priv.MYI help_topic.MYD tables_priv.frm > db.frm help_topic.MYI tables_priv.MYD > db.MYD host.frm tables_priv.MYI > db.MYI host.MYD time_zone.frm > event.frm host.MYI time_zone_leap_second.frm > event.MYD ndb_binlog_index.frm time_zone_leap_second.MYD > event.MYI ndb_binlog_index.MYD time_zone_leap_second.MYI > func.frm ndb_binlog_index.MYI time_zone.MYD > func.MYD plugin.frm time_zone.MYI > func.MYI plugin.MYD time_zone_name.frm > general_log.CSM plugin.MYI time_zone_name.MYD > general_log.CSV proc.frm time_zone_name.MYI > general_log.frm proc.MYD time_zone_transition.frm > help_category.frm proc.MYI time_zone_transition.MYD > help_category.MYD procs_priv.frm time_zone_transition.MYI > help_category.MYI procs_priv.MYD time_zone_transition_type.frm > help_keyword.frm procs_priv.MYI time_zone_transition_type.MYD > help_keyword.MYD servers.frm time_zone_transition_type.MYI > help_keyword.MYI servers.MYD user.frm > help_relation.frm servers.MYI user.MYD > help_relation.MYD slow_log.CSM user.MYI > > > Could you please let me know where I can create a folder called "visiGene"? > /home/mysql$ or /home/mysql/mysql$ > > and I didn't find a folder called "data" It means I will create a new fodler > "/data/visiGene", is it right? > > Then I will copy your files as > rsync -a -P rsync://hgdownload.cse.ucsc.edu/mysql/visiGene/ > /home/mysql/data/visiGene/ > > > Looking forward to hearing from you. > > Best Wishes, > > Yan > ________________________________________ > From: Hiram Clawson [[email protected]] > Sent: Wednesday, May 04, 2011 2:01 PM > To: Luo, Yan (NIH/NHLBI) [C] > Cc: [email protected] > Subject: Re: [Genome] Fail to use "visiGene" > > Good Morning Yan: > > We have failed to mention visiGene in the browser setup procedures. > It is a small database that you can install in your local situation. > > The database can be fetched via rsync directly into your MySQL installation: > > rsync -a -P rsync://hgdownload.cse.ucsc.edu/mysql/visiGene/ > /your/mysql/data/visiGene/ > > --Hiram > > Luo, Yan (NIH/NHLBI) [C] wrote: >> Hi, Mary, >> >> The issue has been fixed by edit the index file, however, we have a new >> error, I believe it is related with the connection of DB. When I click >> "visiGene" (top bar or left bar), I got the following error"Early Error", >> could you please let me know how to fix it? >> >> Couldn't connect to database visiGene on localhost as hguser. Unknown >> database 'visiGene' >> >> Looking forward to hearing from you. >> >> Best Wishes, >> >> Yan > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
