Checking out UCSC Genome Browser Code

Update your .cshrc or .bashrc file to include the project-specific environment variables:

CVSROOT=/projects/compbio/cvsroot
MYSQLLIBS=/usr/lib64/mysql/libmysqlclient.a -lz
MYSQLINC=/usr/include/mysql
PATH=$PATH:/cluster/bin/$MACHTYPE

Use CVS to check out kent/src:

• Log onto hgwdev. Stay in your home directory.
• cvs checkout kent
• produces a source hierarchy under your home directory ~/kent/
• Create a .cvsrc file in your home directory with the lines:

  update -d -P
  co -P
  

• mkdir ~/bin ~/bin/x86_64
• cp /usr/local/apache/cgi-bin/hg.conf .hg.conf
• chmod 600 .hg.conf
• edit .hg.conf to personalize it to your user name and change the read-only MySQL user name to the read-write MySQL user name.
• Set up a daily cron job to keep your source tree up to date. Example dailyCvsUpdate.sh script.

The source will be in kent/src under your home directory.

Built binaries will end up in ~/bin/x86_64 mostly, but you don't want to do this unless you are developing one. CGI binaries will go to /usr/local/apache/cgi-bin-$USER

You will have read-write access to the database (.hg.conf). Be careful.

Highly recommended, make that MANDATORY read the README files in the source tree in
kent/src/product/README.* and kent/src/README, kent/src/hg/makeDb/trackDb/README