The suggestions made below are a best-guess to get your local version of the GPM up and running. Your specific computing environment may require different values than those listed; if you have difficulty getting everything installed, please contact your local technical support.
The directions below assume the versions of Apache, Perl and MySQL to be used were extracted from the archive available on the GPM FTP site.
Text written in fixed-space font denote text to be typed.
Text written in bold are directory paths.
Prerequisites
A fully patched version of a Windows operating system.
A hard drive with several gigabytes of free space.
Obtaining Server Software
Download ftp://ftp.thegpm.org/projects/localgpm/gpm-software.zip This is the directory structure, scripts and support files that will operate the local GPM version, as well as some tools to modify the scripts for your specific location.
Download Apache HTTP Server, ActiveState Perl and MySQL Community Edition.
Or, ftp://ftp.thegpm.org/projects/localgpm/apache-perl-mysql.zip This is a single archive file which contains Apache HTTP Server 2.2.15, ActiveState Perl 5.10.1.1007 and MySQL Server 5.1.48. After downloading, extract the three setup files to a temporary location; you will not need them after installation is complete.
Extract the contents of gpm-software.zip to the location you have chosen. E.g., if the E: drive on your computer has the free space an installation will require, extract gpm-software.zip to E:\. This will create the necessary directory structure and place the scripts required to display information.
Extract the contents of fasta.zip to the folder \thegpm\fasta\ you created in the step above.
Apache Installation
Locate and start the installer, called httpd-2.2.15-win32-x86-openssl-0.9.8m-r2.msi
"Network domain" value should be the same as the end of the target computer's DNS name; e.g., if the target computer has a DNS entry of "science14.med.university.edu", enter "med.university.edu". If you need assistance with this step, contact your local support.
"Server name" value should match the full DNS name of the target computer. E.g., if the computer onto which the local version of the GPM is being installed has a DNS name of "web3.university.edu", enter "web3.university.edu". If you need assistance with this step, contact your local support.
"Administrator's email address" is the email displayed if the web server encounters problems displaying pages.
Choose between having Apache run as a service (will be available whenever the computer is on; recommended), or being manually started and stopped.
Use a "Typical" installation.
Let installation complete.
Perl Installation
Locate the installer called ActivePerl-5.10.1.1007-MSWin32-x86-291969.msi)
Choose a "typical" install using the recommended settings.
MySQL Installation
Locate the installer called mysql-essential-5.1.48-win32.msi.
Choose a "Typical" install.
Choose "Configure the MySQL Server now".
Choose "Detailed Configuration".
Choose "Server Machine".
Choose "Non-transactional Database only".
Choose "Decision Support (DSS)/OLAP".
Choose "Include Bin Directory in Windows PATH".
Enter a root password. Remember this password, as it will be needed later. Complete the configuration.
Configuration
Apache Configuration
Navigate to the Apache installation directory (C:\Program Files\Apache Software Foundation\Apache2.2 by default). Go into the conf directory. Make a backup copy of httpd.conf.
Edit httpd.conf as follows:
The DocumentRoot value is based off wherever you extracted gpm-software.zip. Do a search and replace on everything between the quotes and substitute "<base_path>/thegpm", where <base_path> stands for the path in which you extracted gpm-software.zip. E.g., if you installed to E:\, write "E:/thegpm"; if you installed to "D:/websites/", write "D:/websites/thegpm".
A few lines below the DocumentRoot entry is a line that begins <Directory "<drive_letter>:/path"> There is a note above it regarding changing that value to match the DocumentRoot path. Do so.
In the section marked "<IfModule alias_module>", modify the ScriptAlias value, based off wherever you extracted gpm-software.zip. Make the line read: ScriptAlias /thegpm-cgi/ "<base_path>/thegpm/thegpm-cgi/", where <base_path> stands for the path in which you extracted gpm-software.zip. E.g., if you installed to E:\, write "E:/thegpm/thegpm-cgi/"; if you installed to "D:/websites/", write "D:/websites/thegpm/thegpm-cgi/".
Save the changes and restart the Apache server. If it fails to start, use the command-line Apache tool: "apachectl configtest" in the /bin/ folder of the Apache install directory.
MySQL Configuration
From the Services control panel in the Administrative Tools, stop the MySQL service. Go to the installation directory of MySQL. Make a backup copy of the my.ini file. Open the my.ini file and locate the datadir value.
From My Computer, navigate to the default data directory specified in the datadir value from the step above. Copy all contents of the default data folder (including all subfolders) to <base_path>/gpmdb/data/, where <base_path> is where the gpm-software.zip archive was extracted.
Update the datadir value in the my.ini file to read datadir="<base_path>/gpmdb/data/", including the double quotes, where <base_path> is where the gpm-software.zip archive was extracted.
Save the file and restart the MySQL service.
Perl Configuration
Navigate to the Perl \bin\ directory (by default, this is c:\perl\bin\).
Run the command ppm. This will start the Perl Package Manager.
Display all packages.
In the search box, type dbd-mysql. Choose the resulting package, install it, then exit Perl Package Manager.
Script Configuration
Run the script to edit the path information for all the Perl scripts used. Start a command-line window, and navigate to \thegpm\scripts\ directory. Run the script local_gpm_pathmod.pl by typing perl local_gpm_pathmod.pl <base_path>/thegpm/ where <base_path> is the path to where the gpm-software.zip archive was extracted. Ensure you use front slashes (/) instead of back slashes (\) when typing the path. This will edit scripts in both \thegpm\scripts\ and \thegpm\thegpm-cgi\.
Edit the \thegpm\thegpm-cgi\dbcommon.pl file. In the functions GetUser() and GetPass() define a username and password for the read-only database user (default values are readuser/readpass). In the functions GetRUser() and GetRPass(), do the same for the read/write user (default values are writeuser/writepass). Do not skip this step; the integrity of the database depends on it. Also, it is NOT recommended to use the root username and password you defined during MySQL setup in the dbcommon.pl file.
Edit the \thegpm\thegpm-cgi\defines.pl file.
get_server_name() function: enter the DNS name of the server as the value.
get_gpm_number() function: enter "GPMnnn", where "nnn" is three numerals.
get_proxy() function: (optional); if your network uses a proxy server, enter the URL as the value.
Database Configuration
Edit the file \gpmdb\create_local_gpmdb_users.sql to define the username and password for both a read-only user and a read/write user. They must match what you entered as the usernames and passwords in the \thegpm\thegpm-cgi\dbcommon.pl file.
Edit the file \gpmdb\populate_paths_table.sql the values that define the path in which the result files will be stored. An example line is defined at the top of the file, with the values to use defined in the bottom line. Ensure any paths defined in this file exist in your file system before attempting to submit a file for identification.
Log into MySQL as the root user you defined during its installation, not the read/write user defined in \thegpm\thegpm-cgi\dbcommon.pl and \gpmdb\create_local_gpmdb_users.sql.
Type: "source <base_path>/thegpm/scripts/create_localgpm_databases_tables.sql;" (without the quotes), where <base_path> is the location where gpm-software.zip was extracted; e.g., E:/ or D:/websites/. This will create the GPMDB database and table structure that will be populated after data files are submitted to the identification software.
Type: "source <base_path>/gpmdb/create_local_gpmdb_users.sql;" (without the quotes), where <base_path> is the location where gpm-software.zip was extracted; e.g., E:/ or D:/websites/. This will create the users needed by the Perl scripts to both display and add information to the database.
Type: "source <base_path>/gpmdb/populate_paths_table.sql;" (without the quotes), where <base_path> is the location where gpm-software.zip was extracted; e.g., E:/ or D:/websites/. This will add a path value for all GPM result files created by search software on your installation.
From the DOS prompt, navigate to <base_path>/thegpm/scripts/descriptions/. For each file in the directory, run the command perl <base_path>/thegpm/scripts/add_descriptions_to_map.pl file <file name>. Alternatively, type for /f %f in ('dir /b <base_path>\thegpm\scripts\descriptions\*.txt') do perl <base_path>/thegpm/scripts/add_descriptions_to_map.pl file <base_path>\thegpm\scripts\descriptions\%f, where <base_path> is the location where gpm-software.zip was extracted; e.g., E:/ or D:/websites/. This will add the protein descriptions to enspmapdb for the proteins described in the .fasta files bundled with the installation.
Automation Configuration
Schedule the execution of the \thegpm\temp\gpm_process_master.pl script, which parses the XML files created by the search software and adds them to the database. This can be done in the Windows Control Panel, under Scheduled Tasks.