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== Prerequisites == | == Prerequisites == | ||
- | *A fully patched | + | *A fully patched version of a Windows operating system. |
*A hard drive with several gigabytes of free space. | *A hard drive with several gigabytes of free space. | ||
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**MySQL: http://www.mysql.com/downloads/mirror.php?id=390181#mirrors | **MySQL: http://www.mysql.com/downloads/mirror.php?id=390181#mirrors | ||
**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. | **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. | ||
- | *Download ftp://ftp.thegpm.org/projects/localgpm/fasta.zip | + | *Download ftp://ftp.thegpm.org/projects/localgpm/fasta.zip This a collection of FASTA files for eukaryotes used by the search software when assigning protein identifications. Additional files can be added after installation and are available at ftp://ftp.thegpm.org/projects/xhunter/fasta/ |
== Installation == | == Installation == | ||
*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 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 === | === Apache Installation === | ||
#Locate and start the installer, called '''httpd-2.2.15-win32-x86-openssl-0.9.8m-r2.msi''' | #Locate and start the installer, called '''httpd-2.2.15-win32-x86-openssl-0.9.8m-r2.msi''' | ||
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#Choose a "typical" install using the recommended settings. | #Choose a "typical" install using the recommended settings. | ||
=== MySQL Installation === | === MySQL Installation === | ||
+ | #Locate the installer called '''mysql-essential-5.1.48-win32.msi'''. | ||
#Choose a "Typical" install. | #Choose a "Typical" install. | ||
#Choose "Configure the MySQL Server now". | #Choose "Configure the MySQL Server now". | ||
##Choose "Detailed Configuration". | ##Choose "Detailed Configuration". | ||
##Choose "Server Machine". | ##Choose "Server Machine". | ||
- | ##Choose "Non-transactional Database". | + | ##Choose "Non-transactional Database only". |
##Choose "Decision Support (DSS)/OLAP". | ##Choose "Decision Support (DSS)/OLAP". | ||
##Choose "Include Bin Directory in Windows PATH". | ##Choose "Include Bin Directory in Windows PATH". | ||
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##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"'''. | ##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. | ##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: <tt>ScriptAlias /thegpm-cgi/ "<base_path>/thegpm/thegpm-cgi/"</tt>, where '''<base_path>''' stands for the path in which you extracted gpm-software.zip. E.g., if you installed to | + | ##In the section marked "<IfModule alias_module>", modify the ScriptAlias value, based off wherever you extracted gpm-software.zip. Make the line read: <tt>ScriptAlias /thegpm-cgi/ "<base_path>/thegpm/thegpm-cgi/"</tt>, 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: "<tt>apachectl configtest</tt>" in the '''/bin/''' folder of the Apache install directory. | #Save the changes and restart the Apache server. If it fails to start, use the command-line Apache tool: "<tt>apachectl configtest</tt>" in the '''/bin/''' folder of the Apache install directory. | ||
+ | |||
=== MySQL Configuration === | === 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 <tt>datadir</tt> value. |
- | #From My Computer, navigate to the default data directory specified in the <tt>datadir</tt> | + | #From My Computer, navigate to the default data directory specified in the <tt>datadir</tt> 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 <tt>datadir</tt> value in the my.ini file to read <tt>datadir="<base_path>/gpmdb/data/"</tt>, including the double quotes, where '''<base_path>''' is where the gpm-software.zip archive was extracted. | #Update the <tt>datadir</tt> value in the my.ini file to read <tt>datadir="<base_path>/gpmdb/data/"</tt>, including the double quotes, where '''<base_path>''' is where the gpm-software.zip archive was extracted. | ||
#Save the file and restart the MySQL service. | #Save the file and restart the MySQL service. | ||
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=== Script Configuration === | === 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 <tt>perl local_gpm_pathmod.pl <base_path>/thegpm/</tt> 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\'''. | #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 <tt>perl local_gpm_pathmod.pl <base_path>/thegpm/</tt> 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\'''. | ||
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#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\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. | #Edit the '''\thegpm\thegpm-cgi\defines.pl''' file. | ||
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=== Database Configuration === | === 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\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'''. | *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: "<tt>source <base_path>/thegpm/scripts/create_localgpm_databases_tables.sql;</tt>" (without the quotes), where <base_path> is the location where gpm-software.zip was extracted; e.g., ''' | + | *Type: "<tt>source <base_path>/thegpm/scripts/create_localgpm_databases_tables.sql;</tt>" (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: "<tt>source <base_path>/gpmdb/create_local_gpmdb_users.sql;</tt>" (without the quotes), where <base_path> is the location where gpm-software.zip was extracted; e.g., ''' | + | *Type: "<tt>source <base_path>/gpmdb/create_local_gpmdb_users.sql;</tt>" (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: "<tt>source <base_path>/gpmdb/populate_paths_table.sql;</tt>" (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 <tt>perl <base_path>/thegpm/scripts/add_descriptions_to_map.pl file <file name></tt>. Alternatively, type <tt>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</tt>, 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 === | === Automation Configuration === | ||
- | *Schedule the execution of the '''\thegpm\ | + | *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. |
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