The files that you need to have on /mnt/nfs prior to doing this are:
install-drosophila-stuff.bash - script that automates configuration of MySQL and copying of Drosophila melanogaster files to host, and also copies the CPAN configuration files to host so you can use CPAN
my.cnf - the MySQL config file
gdtile.sql - MySQL schema for 'gdtile' database
dmel-4-r4.2.1.conf - Apache/GBrowse Drosophila melanogaster '.conf' file
dmel-4-r4.2.1 directory - the GBrose database directory for Drosophila melanogaster (containing the FASTA and the GFF file)
TiledImage directory - the SVN 'TiledImage' project
cpan.tar.gz - CPAN files that go to the /root directory on each host
Config.pm - CPAN config file that goes to the /usr/lib/perl5/5.8.5/CPAN directory on each host
bioperl-1.5.1-rc3.tar.gz  - BioPerl source
Generic-Genome-Browser-1.62.tar.gz - GBrowser source

Assuming MySQL is already installed (which it should be on all cluster nodes), do this to configure MySQL and copy TiledImage and Drosophila melanogaster GBrowse files (everything up to the CPAN-requiring steps is part of the install-drosophila-stuff.bash script on /mnt/nfs, aka lorien:/home, so you can just run that instead of each command below):
rm -f /etc/my.cnf
cp /mnt/nfs/my.cnf /etc
/usr/bin/mysql_install_db --user=mysql
/usr/bin/mysqld_safe --user=mysql &
ln -s /tmp/mysql.sock /var/lib/mysql/mysql.sock
cd /home/sgeadmin
mkdir dmel
cd dmel
cp /mnt/nfs/dmel-4-r4.2.1.conf .
cp -R /mnt/nfs/dmel-4-r4.2.1 .
cd ..
cp -R /mnt/nfs/TiledImage .
chown -R sgeadmin:sgeadmin /home/sgeadmin/dmel
chown -R sgeadmin:sgeadmin /home/sgeadmin/TiledImage

The MySQL daemon might take a few seconds to start up, and after it does (which you can check by using 'ps -elf|grep mysql'), add the 'gdtile' database schema to MySQL:
cat /mnt/nfs/TiledImage/gdtile.sql | mysql --user=root

Regarding the CPAN-requiring steps below - new machines won't have CPAN configured on them (the module must be there, but the configuration is not set up yet), but that is easy to fix by just copying the appropriate config files onto the host (this file copying is actually also part of /mnt/nfs/install-drosophila-stuff.bash):
cp /mnt/nfs/cpan.tar.gz /root/
tar xvfz /root/cpan.tar.gz
rm -f /root/cpan.tar.gz
rm -f /usr/lib/perl5/5.8.5/CPAN/Config.pm ; cp /mnt/nfs/Config.pm /usr/lib/perl5/5.8.5/CPAN/

Side note - to change the URL you obtain CPAN modules from, see "Reconfiguring CPAN" section in:
http://sial.org/howto/perl/life-with-cpan/

Install BioPerl and GBrowse (described in more detail in http://biowiki.org/InstallTileRendering):

- install these with CPAN:
  CGI
  CGI::Session
  DBI
  DBD::mysql
  Digest::MD5
  Text::Shellwords
  Bundle::BioPerl (requires interaction to say "yes" to additional modules and to answer some config questions - use defaults for everything)

- install BioPerl from source:
cd /usr/local/src
cp /mnt/nfs/bioperl-1.5.1-rc3.tar.gz .
tar xvfz bioperl-1.5.1-rc3.tar.gz
rm -f bioperl-1.5.1-rc3.tar.gz
cd bioperl-1.5.1-rc3
perl Makefile.PL  # requires interaction to answer config questions - use defaults for everything, except that you might want to run the Bio::DB::GFF tests

- before actualy making BioPerl, install some more modules with CPAN:
  GD::SVG (need to 'force install')
  Ace (requires interaction to say "yes" to additional modules and to answer some config questions - use defaults for everything)
  XML::SAX::Writer (need to 'force install' and requires interaction - use defaults for everything)
  Clone
  Class::AutoClass

- now, actually make BioPerl
make
make test
make install

- install some optional modules with CPAN:
  XML::Twig (need to 'force install' this one and answering some config questions - accept defaults for everything)
  Bio::Das

- install GBrowse from source
cd /usr/local/src
cp /mnt/nfs/Generic-Genome-Browser-1.62.tar.gz .
tar xvfz Generic-Genome-Browser-1.62.tar.gz
rm -f Generic-Genome-Browser-1.62.tar.gz
cd Generic-Genome-Browser-1.62
perl Makefile.PL
make
make test
make install

GBROWSE IS READY TO GO!

Running 'generate-tiles.pl' for the above Drosophila melanogaster-specific setup:
./generate-tiles.pl -c /home/sgeadmin/dmel/ -o /mnt/nfs/dmel -l 4 -p 0 -v 2 --print-tile-nums --no-xml -r [YOUR FAVORITE RANGE] &> /mnt/nfs/dmel/LOG.$jobnum.$hostname &

-- AndrewUzilov - 07 Feb 2006