You have several choices to solve this problem. When you build your MySQL system you can specify the location of the mysql.sock with the build options. If this is the mechanism, you must make sure the build of the kent source uses these new libraries that have this built in mysql.sock location.
You can also specify a mysql.sock location in configuration file options for the MySQL server when you start it up. In this case, you need to have the equivalent options specified for the kent programs in the cgi-bin/hg.conf or your $HOME/.hg.conf file as: db.socket and db.port variables. Note this discussion about these variables in the source tree template src/product/ex.hg.conf You can try a last attempt at fixing this with symlinks for the directories involved to get the real directory appearing at the location that the MySQL system thinks the socket should be. This is a kludge operation and is only a desperate solution. --Hiram Ka-Kyung Kim wrote: > Hello, > > I'm in the process of mirroring a minimal installation of the genome > browser on an ubuntu 10.04 web open tutorial. > (http://enotacoes.wordpress.com/2009/09/03/installing-a-minimal-ucsc-mirror-in-ubuntu-jaunty-64-bits/). > I've met some problems that I cannot solve. > > Fisrt of all, I met the error when I try to connect to the browser > appears as follows: > > Couldn't connect to database (null) on localhost as hguser. > Can't connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (13) > > I've been searching on the mailing list for this issue similar to mine > (such as > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-December/002245.html), > but nothing helps. > In my system, the file '/var/lib/mysql/mysql.sock' doesn't exits, > instead only '/var/run/mysqld/mysqld.sock' exists. > > Secondly, I don't know which filename I should save following contents > in /etc/cron.daily folder in the process of "Setup crontab to clean > trash". > > Create a script at /etc/cron.daily (no . or _ allowed in the file name) > with the following contents: > #!/bin/bash find /var/www/genomebrowser/trash/ \! \( -regex > "/var/www/genomebrowser/trash/ct/.*" \ -or -regex > "/var/www/genomebrowser/trash/hgSs/.*" \) -type f -amin +5040 -exec rm -f > {} \; find /var/www/genomebrowser/trash/ \( -regex > "/var/www/genomebrowser/trash/ct/.*" \ -or -regex > "/var/www/genomebrowser/trash/hgSs/.*" \) -type f -amin +10080 -exec rm -f > {} \; > > Lastly, when I typed "mysql -youraccountoptions -e "create database hgcentral" > The message was shown. > "mysql: unknown option '-y'" > > Do you have any ideas about those errors? > Thank you very much in advance! > > Ka-Kyung _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
