Hi Devasta, Please take a look at current mirror instructions located here:
http://genome.ucsc.edu/admin/mirror.html In a wiki page that is linked within the instructions there is a section that tells what to do "If it doesn't work..." http://genomewiki.ucsc.edu/index.php/Browser_Installation#If_it_doesn.27t_work. .. It states: "*Couldn't connect to database (null) on localhost as readwrite. Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock'*" - try mysql --socket /var/lib/mysql/mysql.sock, if this doesn't work then you have to move your mysql socket (change /etc/mysql/my.cnf) You will need to look at MySQL documentation or use google to find information on how to set the socket location with your system. We are unable to assist with this aspect of the mirror installation. We highly recommend building from source and not using the pre-built binaries from our site which it looks like the instructions you are using state that. Hope that helps! If you have further questions, please email the mailing list: [email protected] Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Devasta Palle <[email protected]> Date: Wed, Nov 9, 2011 at 5:16 PM Subject: [Genome] Local installation of the Genome Browser, MySQL socket issue To: [email protected] Hi, I'm trying to install the genome browser on my debian machine. I'm following this tutorial: http://enotacoes.wordpress.com/2009/09/03/installing-a-minimal-ucsc-mirror-in-ubuntu-jaunty-64-bits/ (also published on http://xiaofeng1982.blog.163.com/blog/static/315724582011627102816454/) Now, I meet the terrible-uncrossable-horrific mysql socket issue: if I point my firefox (I know, it's debian, it should not have firefox, but, whatever) to http://localhost/genomebrowser/cgi-bin/hgGateway I get the following message 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) If I run hgGateway from xterm (after copying /var/www/genomebrowser/cgi-bin/hg.conf to ~/.hg.conf) I get the normal html page of hgGateway. Sincerely, I don't know what to do, neither what to search. Somebody have met the same problem? _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
