m (→Obtaining Server Software) |
m (→Database Configuration) |
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*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. | *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., ''' | + | *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., ''' | + | *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\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. | *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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