TPP:Installing on Ubuntu 7.04

sudo apt-get install build-essential

sudo su
tar xzf httpd-2.2.4.tar.gz
cd httpd-2.2.4
./configure --prefix=/usr/local/apps/apache2
make
make install

cd /usr/local/apps/apache2/conf
mv httpd.conf httpd.conf.original
mv /current/directory/of/httpd.conf.tpp /usr/local/apps/apache2/conf
ln -s httpd.conf.tpp httpd.conf

/usr/local/apps/apache/bin/apachectl -k restart

tar xzf TPP_v3.0.3_SQUALL.zip
cd trans_proteomic_pipeline/src

make configure
make
sudo make install

sudo mkdir /usr/local/apps/tpp/data
sudo chmod 777 /usr/local/apps/tpp/data

sudo ln -s /usr/bin/nice /bin/nice

# This file hosts 2 servers from localhost: 1) TPP and 2) CPAS


# where Apache2 install actually lives on filesystem
ServerRoot "/usr/local/apps/apache2"


# Fully qualified name for server
ServerName localhost

# User accounts to use for Apache processes
<IfModule !mpm_netware_module>
User daemon
Group daemon
</IfModule>

# Contact info. for when people break the machine
ServerAdmin dfermin@umich.edu


# Sets the file Apache will server if a directory is requested
<IfModule dir_module>
	DirectoryIndex index.html
</IfModule>

# Prevents access to .htaccess and .htpasswd files
<FilesMatch "^\.ht">
	Order allow,deny
	Deny from all
	Satisfy All
</FilesMatch>

# Default MIME type the server will use for documents if it can't 
# figure one out for a given file extension
DefaultType text/plain

<IfModule mime_module>
	TypesConfig conf/mime.types
	AddType application/x-compress .Z
	AddType application/x-gzip .gz .tgz
	AddType text/html .shtml
	AddHandler server-parsed .shtml
	AddOutputFilter INCLUDES .shtml
</IfModule>

# Secure (SSL/TLS) connections
<IfModule ssl_module>
SSLRandomSeed startup builtin
SSLRandomSeed connect builtin
</IfModule>


## Ports to listen on for TPP
Listen 80
NameVirtualHost 127.0.0.1:80


## Ports to listen on for CPAS
#Listen 8080
#NameVirtualHost 127.0.0.1:8080


######################### TPP Server Configuration ############################
<VirtualHost 127.0.0.1:80>
	## IP address _AND_ port to access this server on
	ServerName 127.0.0.1:80
	DocumentRoot /usr/local/apps/tpp
	SetEnv WEBSERVER_ROOT /usr/local/apps/tpp
	
	# file where errors are recorded and what level of recording is done
	ErrorLog logs/tpp-errors.log
	LogLevel warn
	
	# Access logs
	<IfModule log_config_module>
		# Directives defining formatting of access log output
		LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined
		LogFormat "%h %l %u %t \"%r\" %>s %b" common

    		<IfModule logio_module>
      			# You need to enable mod_logio.c to use %I and %O
      			LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio
    		</IfModule>
		CustomLog logs/tpp_access_log common
	</IfModule>
	
	

	## Global directives for TPP configuration
	<Directory "/usr/local/apps/tpp">
		Options Indexes FollowSymLinks
		AllowOverride None
		Order allow,deny
		Allow from all
	</Directory>	

	# directory to store data for web browser viewing
	Alias /tpp/data "/usr/local/apps/tpp/data"
	<Directory "/usr/local/apps/tpp/data">
		AllowOverride None
		Options Indexes FollowSymLinks Includes
		Order allow,deny
		Allow from all
	</Directory>

	# directory for tpp's html resources (css, js, images, etc)
	Alias /tpp/html "/usr/local/apps/tpp/html"
	<Directory "/usr/local/apps/tpp/html">
		AllowOverride None
		Options Includes Indexes FollowSymLinks MultiViews
		Order allow,deny
		Allow from all
	</Directory>
	
	# directory for tpp's schema resources
	<Directory "/usr/local/apps/tpp/schema">
		AllowOverride None
		Options Includes Indexes FollowSymLinks MultiViews
   		Order allow,deny
    		Allow from all
	</Directory>
	
	# directory for tpp's executable files
	ScriptAlias /tpp/cgi-bin/ "/usr/local/apps/tpp/cgi-bin/"
	<Directory "/usr/local/apps/tpp/cgi-bin">
    		AllowOverride AuthConfig Limit
    		Options Indexes FollowSymLinks MultiViews ExecCGI +Includes
    		Order allow,deny
    		Allow from all
    		SetEnv WEBSERVER_ROOT /usr/local/apps/tpp
	</Directory>
</VirtualHost>
##############################################################################

########################## CPAS Configuration ################################
# Not relevant to this TPP HowTo so you can delete this section
##############################################################################