removed obsolete scripts

scripts/install/check_environment

-#!/bin/sh
-
-# just remember that the max number of arguments is 9 !!!
-
-for VAR
-do
-	env | grep ^$VAR= > /dev/null
-	if [ $? != 0 ]
-	then
-		echo "\$$VAR not set."
-		exit
-	fi
-done

scripts/install/configure_cpan.pl

-use CPAN;
-
-my $FTP = find_path('ftp');
-my $GZIP = find_path('gzip');
-my $LYNX = find_path('lynx');
-my $MAKE = find_path('make');
-my $NCFTPGET = find_path('ncftpget');
-my $NCFTP = find_path('ncftp');
-my $LESS = find_path('less');
-my $TAR = find_path('tar');
-my $UNZIP = find_path('unzip');
-my $WGET = find_path('wget');
-
-my $conf = bless {}, CPAN::Config;
-$CPAN::Config->{'build_cache'} = 10;
-$CPAN::Config->{'build_dir'} = "$ENV{'HOME'}/.cpan/build";
-$CPAN::Config->{'cache_metadata'} = 1;
-$CPAN::Config->{'cpan_home'} = "$ENV{'HOME'}/.cpan";
-$CPAN::Config->{'ftp'} = $FTP;
-$CPAN::Config->{'ftp_proxy'} = q[];
-$CPAN::Config->{'getcwd'} = q[cwd];
-$CPAN::Config->{'gzip'} = $GZIP;
-$CPAN::Config->{'http_proxy'} = q[];
-$CPAN::Config->{'inactivity_timeout'} = q[0];
-$CPAN::Config->{'index_expire'} = q[1];
-$CPAN::Config->{'inhibit_startup_message'} = q[0];
-$CPAN::Config->{'keep_source_where'} = "$ENV{'HOME'}/.cpan/sources";
-$CPAN::Config->{'lynx'} = $LYNX;
-$CPAN::Config->{'make'} = $MAKE;
-$CPAN::Config->{'make_arg'} = q[];
-$CPAN::Config->{'make_install_arg'} = q[];
-$CPAN::Config->{'makepl_arg'} = q[];
-$CPAN::Config->{'ncftpget'} = $NCFTPGET;
-$CPAN::Config->{'ncftp'} = $NCFTP;
-$CPAN::Config->{'no_proxy'} = q[];
-$CPAN::Config->{'pager'} = $LESS;
-$CPAN::Config->{'prerequisites_policy'} = q[follow];
-$CPAN::Config->{'scan_cache'} = q[atstart];
-$CPAN::Config->{'shell'} = $ENV{'SHELL'};
-$CPAN::Config->{'tar'} = $TAR;
-$CPAN::Config->{'term_is_latin'} = 1;
-$CPAN::Config->{'unzip'} = $UNZIP;
-$CPAN::Config->{'urllist'} = [];
-$CPAN::Config->{'wait_list'} = [q[wait://ls6.informatik.uni-dortmund.de:1404]];
-$CPAN::Config->{'wget'} = $WGET;
-
-$conf->commit($ARGV[0]);
-
-
-sub find_path {
-    my $prog = shift;
-    my $path = `which $prog`;
-    chomp $path;
-    $path =~ s/\033.*\007//;
-    if ($path =~ /(no $prog in|Comman not found)/) {
-	return;
-    } else {
-	return $path;
-    }
-}

scripts/install/configure_defs.pl

-use strict;
-
-foreach (@ARGV) {
-	reconfigure($_);
-}
-
-sub reconfigure {
-	my $file = shift;
-	open IN, $file or die "Cant open $file: $!\n";
-	local $/ = undef;
-	my $txt = <IN>;
-	close IN;
-	foreach my $k (keys %ENV) {
-	    $k =~ /^ENSEMBL_/ || next;
-	    $txt =~ s/(\$${k}\s*?=).*?\n/$1 '$ENV{$k}';\n/gs;
-	}
-	open OUT, ">$file" or die "Cant write to $file: $!\n";
-	print OUT $txt;
-	close OUT;
-}

scripts/install/create_directories

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment ROOTDIR SRCDIR MANDIR LIBDIR BINDIR ENSEMBL_SERVERROOT
-
-if [ ! -d $ROOTDIR ]
-then
-	mkdir $ROOTDIR
-	if [ $? != 0 ]
-	then
-		echo "Not able to create $ROOTDIR"
-		exit
-	fi
-fi
-
-if [ ! -d $SRCDIR ]
-then
-    mkdir $SRCDIR
-fi
-if [ ! -d $MANDIR ]
-then
-    mkdir $MANDIR
-fi
-if [ ! -d $LIBDIR ]
-then
-    mkdir $LIBDIR
-fi
-if [ ! -d $BINDIR ]
-then
-    mkdir $BINDIR
-fi
-
-if [ ! -d $ENSEMBL_SERVERROOT ]
-then
-    mkdir $ENSEMBL_SERVERROOT
-fi
-
-if [ ! -d $HOME/.cpan ]
-then
-    mkdir $HOME/.cpan
-fi
-
-if [ ! -d $HOME/.cpan/CPAN ]
-then
-    mkdir $HOME/.cpan/CPAN
-fi
-
-if [ ! -d $HOME/.cpan/build ]
-then
-    mkdir $HOME/.cpan/build
-fi
-
-if [ ! -d $HOME/.cpan/sources ]
-then
-    mkdir $HOME/.cpan/sources
-fi

scripts/install/install_apache

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment SRCDIR PERL ENSEMBL_SERVERROOT APACHE_VERSION
-
-# get and unpack mod_perl
-echo
-echo "Downloading mod_perl"
-echo
-cd $HOME/.cpan/build
-wget http://www.perl.com/cgi-bin/cpan_mod?module=mod_perl --passive-ftp
-gtar xvzf mod_perl*
-rm mod_perl*.tar.gz
-#wget http://$CPAN_SITE/modules/by-module/Apache/$MODPERL_VERSION.tar.gz
-#gtar xvzf $MODPERL_VERSION.tar.gz
-
-# get and unpack Apache
-echo
-echo "Downloading Apache"
-echo
-cd $SRCDIR
-wget http://httpd.apache.org/dist/httpd/$APACHE_VERSION.tar.gz --passive-ftp
-gtar xvzf $APACHE_VERSION.tar.gz
-rm $APACHE_VERSION.tar.gz
-# install mod_perl
-echo
-echo "Installing mod_perl"
-echo
-cd $HOME/.cpan/build/mod_perl*
-$PERL Makefile.PL APACHE_SRC=$SRCDIR/$APACHE_VERSION/src DO_HTTPD=1 USE_APACI=1 EVERYTHING=1 
-make
-make test
-make install
-
-# install Apache
-echo
-echo "Installing Apache"
-echo
-cd $SRCDIR/$APACHE_VERSION
-./configure \
-	--prefix=$ENSEMBL_SERVERROOT \
-	--with-perl=$PERL \
-	--activate-module=src/modules/perl/libperl.a
-make
-make install
-
-# conf and htdocs will come from ensembl-mirror, i.e. basically we could
-# remove them at this point
-mv $ENSEMBL_SERVERROOT/conf $ENSEMBL_SERVERROOT/conf.apache
-mv $ENSEMBL_SERVERROOT/htdocs $ENSEMBL_SERVERROOT/htdocs.apache

scripts/install/install_biomodules

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment ENSEMBL_SERVERROOT PERL ENSEMBL_DB_BRANCH ENSEMBL_WEB_BRANCH ENSEMBL_BIOPERL_BRANCH
-
-cd $ENSEMBL_SERVERROOT
-
-# get ensembl-api
-echo
-echo "Installing ensembl-api"
-echo
-cat << _HERE_ | cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/CVSmaster co -r $ENSEMBL_DB_BRANCH ensembl-api
-CVSUSER
-_HERE_
-
-# get ensembl-web
-echo
-echo "Installing ensembl-web"
-echo
-cat << _HERE_ | cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/CVSmaster co -r $ENSEMBL_WEB_BRANCH ensembl-web
-CVSUSER
-_HERE_
-
-# get bioperl
-echo
-echo "Installing Bioperl"
-echo
-cat << _HERE_ | cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl co -r $ENSEMBL_BIOPERL_BRANCH bioperl-live
-cvs
-_HERE_
-
-# get and install das
-echo
-echo "Installing Bio::Das"
-echo
-cat << _HERE_ | cvs -d :pserver:cvs@cvs.biodas.org:/home/repository/biodas checkout das
-cvs    
-_HERE_
-cd das/Bio-Das
-$PERL Makefile.PL
-make && make install
-cd ../..
-
-# create missing dirs
-echo
-echo "Creating missing directories"
-echo
-mkdir htdocs/gfx/clone
-mkdir htdocs/gfx/gene
-mkdir htdocs/gfx/image_tmp
-
-echo
-echo "Reconfiguring httpd.conf"
-echo
-mv conf/httpd.conf conf/httpd.conf.ori
-$PERL -pe 's/^\#!\S+perl/\#\!$ENV{'PERL'}/' < conf/httpd.conf.ori > conf/httpd.conf
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

scripts/install/install_everything

-#!/bin/sh
-
-CONFIGFILE=$1
-
-if [ ! $CONFIGFILE ]
-then
-	echo "Usage: $0 set_environment"
-	exit
-fi
-
-. $CONFIGFILE
-
-if [ ! $INSTALLSCRIPTDIR ]
-then
-	echo "\$INSTALLSCRIPTDIR not set. Don't know where the scripts are."
-	exit
-fi
-
-
-. $INSTALLSCRIPTDIR/create_directories
-. $INSTALLSCRIPTDIR/install_perl
-. $INSTALLSCRIPTDIR/check_environment PERL
-$PERL $INSTALLSCRIPTDIR/configure_cpan.pl $HOME/.cpan/CPAN/MyConfig.pm
-. $INSTALLSCRIPTDIR/install_apache
-. $INSTALLSCRIPTDIR/install_mysql
-. $INSTALLSCRIPTDIR/install_perlmodules
-. $INSTALLSCRIPTDIR/install_biomodules
-. $INSTALLSCRIPTDIR/check_environment ENSEMBL_SERVERROOT
-$PERL $INSTALLSCRIPTDIR/configure_defs.pl $ENSEMBL_SERVERROOT/conf/SiteDefs.pm
-$PERL $INSTALLSCRIPTDIR/configure_defs.pl $ENSEMBL_SERVERROOT/conf/Homo_sapiens_Defs.pm
-$ENSEMBL_SERVERROOT/bin/apachectl start
-

scripts/install/install_mysql

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment SRCDIR BINDIR ENSEMBL_DBPASS
-
-cd $SRCDIR
-
-# get and install MySQL
-echo
-echo "Installing mysql"
-echo
-
-MYSQLVERSION=${MYSQLVERSION:-mysql-3.23.40}
-echo "Downloading MySQL [$MYSQLVERSION]"
-wget http://download.sourceforge.net/mysql/$MYSQLVERSION.tar.gz
-gtar xvzf $MYSQLVERSION.tar.gz
-rm $MYSQLVERSION.tar.gz
-echo "cd $MYSQLVERSION"
-cd $MYSQLVERSION
-echo "./configure --prefix=$ROOTDIR"
-./configure --prefix=$ROOTDIR #\
-			      #--without-server
-# Uncomment above to install just client and libs
-echo "make"
-make
-echo "make test"
-make test
-echo "make install"
-make install
-echo "scripts/mysql_install_db"
-scripts/mysql_install_db 
-# start MySQL daemon
-echo "$BINDIR/safe_mysqld &"
-$BINDIR/safe_mysqld &
-# wait for the server to start up
-sleep 5
-# set the root password
-if [ "$ENSEMBL_DBPASS" != "" ]
-then
-    $BINDIR/mysqladmin -u root --password='' password $ENSEMBL_DBPASS
-fi
-export MYSQL_INCLUDE_DIR=$ROOTDIR/include/mysql
-export MYSQL_LIB_DIR=$ROOTDIR/lib/mysql
-
-#Leave it on for testing
-#$BINDIR/mysqladmin -u root -p$ENSEMBL_DBPASS shutdown

scripts/install/install_perl

-#!/bin/sh
-
-# source this one to get $PERL set
-
-$INSTALLSCRIPTDIR/check_environment SRCDIR CC CPAN_SITE
-
-cd $SRCDIR
-
-# get perl
-echo "wget http://$CPAN_SITE/src/stable.tar.gz"
-wget http://$CPAN_SITE/src/stable.tar.gz --passive-ftp
-
-# unpack it an store the log for extracting the dir name
-gtar xvzf stable.tar.gz > $PID.tmp 2>&1
-rm stable.tar.gz
-
-# extract the dir name
-PERLDIR=`sed '1 q' < $PID.tmp`
-rm $PID.tmp
-
-echo "PERLDIR is $PERLDIR"
-cd $PERLDIR
-# run configure script
-echo "sh Configure -Dprefix=$ROOTDIR -Dcc=$CC -Uinstallusrbinperl -des"
-sh Configure -Dprefix=$ROOTDIR -Dcc=$CC -Uinstallusrbinperl -des
-echo "make"
-make
-echo "make test"
-make test
-echo "make install"
-make install
-echo "cd ../.."
-cd ../..
-export PERL=$ROOTDIR/bin/perl
-
-if [ ! -x $PERL ]
-then
-    echo "$PERL does not exist or is not executable."
-    echo "Something hs gobe wrong with perl installation."
-    exit
-fi

scripts/install/install_perlmodules

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment ROOTDIR PERL GD_VERSION EXPAT_VERSION MYSQL_INCLUDE_DIR MYSQL_LIB_DIR
-
-# configure CPAN stuff
-echo
-echo "Creating ~/.cpan/CPAN/MyConfig.pm"
-echo
-$PERL $INSTALLSCRIPTDIR/configure_cpan.pl ~/.cpan/CPAN/MyConfig.pm
-
-# install URI, Net::FTP, MIME::Base64, Digest::MD5, HTML::Tagset,
-# HTML::Parser, HTML::HeadParser and LWP
-echo
-echo "Installing Bundle::LWP"
-echo
-$PERL -MCPAN -e 'install Bundle::LWP' < /dev/null  
-
-# download DBD::mysql and DBI
-# NOTE: installation of DBD::mysql does not work here, since
-# location of mysql headers and libs are not known by default
-echo
-echo "Installing Bundle::DBD::mysql"
-echo
-$PERL -MCPAN -e 'install Bundle::DBD::mysql'     
-
-# install DBD::mysql
-cd $HOME/.cpan/build/DBD-mysql*
-$PERL Makefile.PL \
-	--cflags=-I$MYSQL_INCLUDE_DIR \
-	--libs="-L$MYSQL_LIB_DIR -lmysqlclient -lz"
-#	--cflags=-I$ROOTDIR/include/mysql \
-#	--libs="-L$ROOTDIR/lib/mysql -lmysqlclient -lz"
-
-make
-make test
-make install
-
-# download and install GD-1.18
-echo
-echo "Installing GD"
-echo
-cd $HOME/.cpan/build
-wget http://$CPAN_SITE/modules/by-authors/Lincoln_D_Stein/$GD_VERSION.tar.gz --passive-ftp
-gtar xvzf $GD_VERSION.tar.gz
-rm $GD_VERSION.tar.gz
-cd $GD_VERSION
-$PERL Makefile.PL
-make
-make test
-make install
-
-# expat, necessary for XML::Parser
-echo
-echo "Installing expat"
-echo
-cd $ROOTDIR/src
-wget http://download.sourceforge.net/expat/$EXPAT_VERSION.tar.gz --passive-ftp
-gtar xvzf $EXPAT_VERSION.tar.gz
-rm $EXPAT_VERSION.tar.gz
-cd $EXPAT_VERSION
-./configure --prefix=$ROOTDIR
-make
-make install
-
-# XML::Parser
-echo
-echo "Installing XML::Parser"
-echo
-cd $HOME/.cpan/build
-$PERL -MCPAN -e 'get XML::Parser'
-cd $HOME/.cpan/build/XML-Parser*
-$PERL Makefile.PL \
-	EXPATLIBPATH=$ROOTDIR/lib \
-	EXPATINCPATH=$ROOTDIR/include
-make
-make test
-make install
-
-# Storable
-# Can't use cpan shell for some reason !?
-echo
-echo "Installing Storable"
-echo
-cd $HOME/.cpan/build
-wget http://www.perl.com/cgi-bin/cpan_mod?module=Storable --passive-ftp
-gtar xvzf Storable*
-rm Storable*.tar.gz
-cd Storable*
-$PERL Makefile.PL
-make
-make test
-make install
-
-# install Apache::DBI
-echo
-echo "Installing Apache::DBI"
-echo
-$PERL -MCPAN -e 'install Apache::DBI'
-
-# install IO::String
-echo
-echo "Installing IO::String"
-echo
-$PERL -MCPAN -e 'install IO::String'
-
-
-

scripts/install/install_web_mirror

-#!/bin/sh
-
-CONFIGFILE=$1
-
-if [ ! $CONFIGFILE ]
-then
-	echo "Usage: $0 set_environment"
-	exit
-fi
-
-. $CONFIGFILE
-
-if [ ! $INSTALLSCRIPTDIR ]
-then
-	echo "\$INSTALLSCRIPTDIR not set. Don't know where the scripts are."
-	exit
-fi
-
-
-. $INSTALLSCRIPTDIR/create_directories
-if [ "$PERL" = "" ] || [ ! -x $PERL ] ; then
-    . $INSTALLSCRIPTDIR/install_perl
-fi
-. $INSTALLSCRIPTDIR/check_environment PERL
-
-$PERL $INSTALLSCRIPTDIR/configure_cpan.pl $HOME/.cpan/CPAN/MyConfig.pm
-if [ "$MYSQL_INCLUDE_DIR" = "" ] || [ "$MYSQL_LIB_DIR" = "" ] ; then
-    . $INSTALLSCRIPTDIR/install_mysql
-fi
-. $INSTALLSCRIPTDIR/check_environment MYSQL_INCLUDE_DIR MYSQL_LIB_DIR
-
-. $INSTALLSCRIPTDIR/install_perlmodules
-. $INSTALLSCRIPTDIR/install_apache
-. $INSTALLSCRIPTDIR/check_environment BINDIR
-# shut down the mysql daemon (was left on for testing)
-$BINDIR/mysqladmin -u root --password='' shutdown
-. $INSTALLSCRIPTDIR/install_biomodules
-. $INSTALLSCRIPTDIR/check_environment ENSEMBL_SERVERROOT
-$PERL $INSTALLSCRIPTDIR/configure_defs.pl $ENSEMBL_SERVERROOT/conf/SiteDefs.pm
-$PERL $INSTALLSCRIPTDIR/configure_defs.pl $ENSEMBL_SERVERROOT/conf/Homo_sapiens_Defs.pm
-$ENSEMBL_SERVERROOT/bin/apachectl start
-
-echo
-echo "Now forward local port $FORWARDED_DB_PORT to port 3306 of the DB server."
-echo
-echo "e.g.: ssh -L $FORWARDED_DB_PORT:$DB_HOST:3306 computer.in.dbhost.domain"
-echo

scripts/install/load_databases

-#!/bin/sh
-
-. $INSTALLSCRIPTDIR/check_environment ENSEMBL_HOST ENSEMBL_DBUSER ENSEMBL_DBPASS ENSEMBL_HOST_PORT BINDIR
-
-mysqladmin=$BINDIR/mysqladmin
-mysql=$BINDIR/mysql
-mysqlimport=$BINDIR/mysqlimport 
-
-
-SCHEMA_GZ=*.sql.gz
-echo $SCHEMA_GZ
-DB_NAME=`echo $SCHEMA_GZ | sed 's/\.sql\.gz//'`
-echo $DB_NAME
-
-$mysqladmin \
-    -u $ENSEMBL_DBUSER \
-    -h $ENSEMBL_HOST \
-    -p$ENSEMBL_DBPASS \
-    -P $ENSEMBL_HOST_PORT \
-    create $DB_NAME
-
-if [ $? != 0 ]; then
-    echo "Creating $DB_NAME failed! Exiting."
-    exit 1
-fi
-
-gunzip -c $SCHEMA_GZ | \
-    $mysql \
-	-u $ENSEMBL_DBUSER \
-	-h $ENSEMBL_HOST \
-	-p$ENSEMBL_DBPASS \
-	-P $ENSEMBL_HOST_PORT \
-	$DB_NAME
-
-if [ $? != 0 ]; then
-    echo "Table creation failed! Exiting."
-    exit 2
-fi
-
-# all tables except dna
-for i in *table.gz; do
-    TABLE=`echo $i | sed 's/\.gz//;'`
-    echo $TABLE
-    echo mkfifo $TABLE
-    `mkfifo $TABLE`
-    echo "gunzip -c $i > $TABLE &"
-    `gunzip -c $i > $TABLE` &
-    $mysqlimport \
-	-u $ENSEMBL_DBUSER \
-	-h $ENSEMBL_HOST \
-	-p$ENSEMBL_DBPASS \
-	-P $ENSEMBL_HOST_PORT \
-	$DB_NAME $TABLE
-    rm -f $TABLE
-    if [ $? != 0 ]; then
-	echo "Importing $TABLE failed! Exiting."
-	exit 3
-    fi
-done
-
-# dna table
-DNA_FILES=`ls dna-table*.gz 2>/dev/null`
-if [ "$DNA_FILES" != "" ]; then
-    echo $DNA_FILES
-    echo mkfifo dna.txt.table
-    `mkfifo dna.txt.table`
-    echo "gunzip -c dna-table*.gz > dna.txt.table &"
-    `gunzip -c dna-table*.gz > dna.txt.table` &
-    $mysqlimport \
-	-u $ENSEMBL_DBUSER \
-	-h $ENSEMBL_HOST \
-	-p$ENSEMBL_DBPASS \
-	-P $ENSEMBL_HOST_PORT \
-	$DB_NAME dna.txt.table
-    rm -f dna.txt.table
-    if [ $? != 0 ]; then
-	echo "Importing dna.txt.table failed! Exiting."
-	exit 4
-    fi    
-fi
-

scripts/install/set_environment

-#!/bin/sh
-
-#various directories
-export INSTALLSCRIPTDIR=$HOME/installscripts
-export ROOTDIR=$PWD
-export SRCDIR=$ROOTDIR/src
-export MANDIR=$ROOTDIR/man
-export LIBDIR=$ROOTDIR/lib
-export BINDIR=$ROOTDIR/bin
-export ENSEMBL_SERVERROOT=$ROOTDIR/ensemblroot
-
-# compiler to be used
-export CC=cc
-
-# 
-export CPAN_SITE=cpan.org
-
-#things to be installed
-export EXPAT_VERSION=expat-1.95.1
-export STORABLE_VERSION=Storable-1.0.13
-export MYSQL_VERSION=mysql-3.23.40
-export MODPERL_VERSION=mod_perl-1.26
-export APACHE_VERSION=apache_1.3.20
-export GD_VERSION=GD-1.18
-export ENSEMBL_DB_BRANCH=branch-ensembl-110
-export ENSEMBL_WEB_BRANCH=branch-ensembl-112
-export ENSEMBL_BIOPERL_BRANCH=branch-07
-
-# mysql server related
-# if envs MYSQL_TCP_PORT and MYSQL_UNIX_PORT are set, mysql daemon
-# is started up with this port and socket
-# define LOCAL_DB_PASS in your shell
-export MYSQL_ROOT=root
-export MYSQL_PASS=$LOCAL_DB_PASS
-export MYSQL_TCP_PORT=3307
-export MYSQL_UNIX_PORT=/tmp/my_own_mysqld.sock
-
-
-# web server related
-export ENSEMBL_USER=$USER
-export ENSEMBL_GROUP=$GROUP
-export ENSEMBL_SERVERADMIN=vastrik@ebi.ac.uk
-export ENSEMBL_PORT=8080
-export ENSEMBL_SERVERNAME=$HOST
-export ENSEMBL_MAIL_ERRORS=$ENSEMBL_SERVERADMIN
-
-#
-# location of databases, usernames, passwds
-#
-# "main" dbs
-export ENSEMBL_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_DBUSER=$MYSQL_ROOT
-export ENSEMBL_DBPASS=$MYSQL_PASS
-export ENSEMBL_HOST_PORT=$MYSQL_TCP_PORT
-
-# userdb
-export ENSEMBL_USERDB_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_USERDB_USER=$MYSQL_ROOT
-export ENSEMBL_USERDB_PASS=$ENSEMBL_DBPASS      
-
-# help db
-export ENSEMBL_HELP_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_HELP_DBUSER=$MYSQL_ROOT
-export ENSEMBL_HELP_DBPASS=$ENSEMBL_DBPASS
-export ENSEMBL_HELP_PORT=$MYSQL_TCP_PORT
-

scripts/install/use_ensrv1.conf

-#!/bin/sh
-
-export FORWARDED_DB_PORT=3306
-export DB_HOST=ensrv1.sanger.ac.uk
-
-#various directories
-export INSTALLSCRIPTDIR=$HOME/installscripts
-export ROOTDIR=$PWD
-export SRCDIR=$ROOTDIR/src
-export MANDIR=$ROOTDIR/man
-export LIBDIR=$ROOTDIR/lib
-export BINDIR=$ROOTDIR/bin
-export ENSEMBL_SERVERROOT=$ROOTDIR/ensemblroot
-
-# compiler to be used
-export CC=cc
-
-# CPAN download site
-export CPAN_SITE=cpan.org
-
-#things to be installed
-export EXPAT_VERSION=expat-1.95.1
-export MYSQL_VERSION=mysql-3.23.40
-export MODPERL_VERSION=mod_perl-1.26
-export APACHE_VERSION=apache_1.3.20
-export GD_VERSION=GD-1.18
-export ENSEMBL_DB_BRANCH=branch-ensembl-110
-export ENSEMBL_WEB_BRANCH=branch-ensembl-112
-export ENSEMBL_BIOPERL_BRANCH=branch-07
-
-# web server related
-export ENSEMBL_USER=$USER
-export ENSEMBL_GROUP=$GROUP
-export ENSEMBL_SERVERADMIN=vastrik@ebi.ac.uk
-export ENSEMBL_PORT=8080
-export ENSEMBL_SERVERNAME=$HOST
-export ENSEMBL_MAIL_ERRORS=$ENSEMBL_SERVERADMIN
-
-#
-# location of databases, usernames, passwds
-#
-# "main" dbs
-export ENSEMBL_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_DBUSER='ensro'
-export ENSEMBL_DBPASS=''
-export ENSEMBL_HOST_PORT=$FORWARDED_DB_PORT
-
-# userdb
-export ENSEMBL_USERDB_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_USERDB_USER=''
-export ENSEMBL_USERDB_PASS=''
-
-# help db
-export ENSEMBL_HELP_HOST=$ENSEMBL_SERVERNAME
-export ENSEMBL_HELP_DBUSER=ensro
-export ENSEMBL_HELP_DBPASS=''
-export ENSEMBL_HELP_PORT=$FORWARDED_DB_PORT
-