#@(#)include.cfg version: 2.50 #======================================================# # Make2D-DB II tool # # include.cfg - configuration file for make2db.pl # #======================================================# #----------------------------------------------------# # START TO SET YOUR CONFIGURATION STARTING FROM HERE # #----------------------------------------------------# # DATABASE OWNER # # The postgreSQL main user (or your postgreSQL user name! being the main owner of the new database and having full write permissions) # if the postgreSQL main user is set to 'default' the name (system login ID) of the actual user will be used # $postgres_user = "khaled"; # Password for the postgreSQL main user: # $postgres_user_password = ''; # Location of the postgres binaries (programs): # (not required, except if you are running postgres programs (e.g. postmaster) from some location other than the default PATH) # $POSTGRES::bin = ''; # Specify the postgres TCP port or the local Unix-domain socket file # extension on which the server is listening for connections. # By default, this value is '5432' # $POSTGRES::port = '5432'; #---------------------------------------# # DATABASE SELECT USER # # PostgreSQL select user (the tool will create this user with no write permissions, only to query the database) # $select_user = "select2d"; # PostgreSQL select user password, if not specified, the password will be set up identical to the select user name # (adapted to pg_hba.conf with password parameters -> no trust) # $select_user_password = ""; #---------------------------------------# # PERL # # PERL Location (for the CGI server scripts to run) # The PERL you are currently using has been detected at the following path: # $perl = "/usr/bin/perl"; # Is the Perl *libwww-perl* module installed (LWP)? or is Perl 5.6 or Active Perl installed (0 for no, 1 for y)? # If not, set $libwww to 0. Doing so will imply desactivation of all external http connections to collect external data. # Information about this module can be found within this package in the 'libs' directory. # (For an up-to-date version of the module, visit 'http://search.cpan.org/dist/libwww-perl/') # $libwww = 1; # Is the Perl *XML::Parser* (XML-Parser), *XML::Parser::PerlSax* (libxml-perl) and *XML::Twig (XML-Twig) # modules installed (0 for no, 1 for y)? # If none of them is installed, set $libxml to 0. Doing so will desactivate all XML parsing and write operations: # e.g. not reading Melanie XML files or not exporting queries in XML format. # Information about those modules can be found within this package in the 'libs' directory. # (For an up-to-date version of the modules, visit 'http://search.cpan.org/~coopercl/XML-Parser/', # 'http://search.cpan.org/~kmacleod/libxml-perl/' and 'http://search.cpan.org/~mirod/XML-Twig/') # $libxml = 1; #---------------------------------------# # PATHS & LOCATIONS # # Path of the directory containing your data: flat file, reports, images and (annotated) maps # $data_dir = "/windows/win-share/khaled/Projects/Make2D-DB_II/data_test"; # Name of your existing *flat file* (data file), including its extension (e.g. my_flat_file.dat). # If you are using spreadsheets (e.g. EXCEL reports), then do not define any name here! # If you are using (Melanie) XML exports and have no flat file, the tool will generate one if you do not definie any file here! # $db_file = ""; # Name of the file listing the maps names, coordinates and other annotations: # $maps_file = "existing.maps"; # A name for your (postgreSQL) database to be created: # when the DB name is set to 'default', the name of the new database will be read from the first line of the database flat file (if any) # Otherwise, define a valid name for your database here! # This name will be *lower-cased* to suite the postgreSQL pgsl program. # Note also that only alphanumeric characters and underscores will be retained. # $database_name = 'test_2dpage'; #---------------------------------------# # BEHAVIOUR # # Do you use Melanie / ImageMaster(TM) 2D Platinum annotated maps (0 for no / 1 for yes)? # If you provide Melanie / ImageMaster(TM) 2D Platinum XML/text reports for the spots' data then set this value to 1. # The tool may try to extract data directly from your Melanie / ImageMaster(TM) 2D Platinum annotated maps if this value is set to 1 and no reports are found. # $Melanie = 0; # Do you want to include in your database non identified spots? # (0 for no / 1 for yes) # $include_not_identified_spots = 1; # if you do not extract spots' positions directly from the Melanie / ImageMaster(TM) 2D Platinum annotated maps, # give a default value (in pixels) for the spots X position on the viewer (for SDS maps): # $default_SDS_x = 200; # Prefix given for the spot IDs: # # The spot IDs listed in the spots position reports should be *exactly* the same as those used in your flat file (the text data file). # If this is not the case, and if your spot IDs used in the flat file include an extra prefix not present in your spots position reports, # then give the expected prefix string here. Leave blank otherwise. # (e.g. if a spot ID *444* in the report corresponds to a spot ID *2D-444* in the flat file, then the prefix should be *2D-*) # $spot_ID_prefix = ''; # EXPASY SERVER URL to address during installation: choose any of the following: # # # $expasy = "http://www.expasy.org"; # # $expasy = "http://cn.expasy.org"; # # $expasy = "http://bo.expasy.org"; # # $expasy = "http://ca.expasy.org"; # # $expasy = "http://au.expasy.org"; # # $expasy = "http://br.expasy.org"; # $expasy = "http://www.expasy.org"; # EXTERNAL DATA BEHAVIOUR # # Include external data (Swiss-Prot, Newt, SWISS-2DPAGE, etc..) by connecting to the Expasy server # (0 for no / 1 for yes)? # this has only effect if $libwww is set to 1, otherwise it will be ignored # * for commercials, check the 'readme/Copyright for external data.txt' file * # $include_sp_external_data = 1; #---------------------------------------# # DEFAULT values for MISSING REQUIRED LINES: RELEASE lines (DT lines) # # (the tool will use those default values if they are missing from the text files) # # creation date of the entries (default date): # $dt_cr_default = "6-Dec-2005"; # creation release (default, minimum = 1): # $dt_cr_num_default = 1; # last update of entries (default date): # $dt_up_default = "6-3-2006"; # update release (default, minimum = 1) # you may use a sub release (e.g. '1.5' for release 1, sub release 5) # $dt_up_num_default = 1.1; #---------------------------------------# # DEFAULT values for MISSING REQUIRED LINES: SPECIES lines (OS, OC, OX lines) # # (the tool will use those default values if they are missing from the text files) # # OS line: species common name (e.g: Human, Mouse, etc.) # $os_default = 'Oryctolagus cuniculus (Rabbit)'; # OC line: organism classification / taxonomy (the standard separator ';' is displayed as a simple comma ',' for security resaons) # $oc_default = 'parent, child'; # OX: organism/species taxonomy ID (NCBI), you can enter 'NCBI_TaxID=number' or simply type directly the ID value, e.g 1000 # $ox_default = '9986'; #---------------------------------------# # DEFAULT values for MISSING REQUIRED LINES: IMAGES line (IM line) # # (the tool will use those default values if they are missing from the text files) # # IM line: Image(s) name(s) (use ',' as separator) # $im_default = 'PLASMA'; #---------------------------------------# # DEFAULT values for MISSING REQUIRED LINES: BIBLIOGRAPHY REFERENCES lines (RP, RA, RL lines) # # You are encouraged to fill those reference values according to your personal work # # Yo may refere to the SWISS-2DPAGE documentation for the precise definition of the syntax to use # # (the tool will use those default values if they are missing from the text files) # # RP line: extent of the work: # $rp_default = '2D GEL CHARACTERIZATION'; # RA line: authors (separated by ','): # $ra_default = 'Author 1., Author 2.'; # RL line: refernece location: # $rl_default = "Submitted (JUN-2006) to the Current database"; #---------------------------------------# # SERVER DIRECTORIES TO QUERY THE DATABASE # # (The 2d sub-directories will be created by the tool, provided that you have write permissions into the server tree) # # main path to the server (Apache Document Root): # $web_server_dir = "/var/www"; # reference name for the directories containing your data in the server: # (not the full path! this name will be given to different sub-directories in the server directory tree) # (you can give the name of your database, making sure it does not contain spaces nor special characters) # ('-' are tolerated: e.g. swiss-2dpage or 'my-2dpage') # $web_server_ref_name = "2d"; # path for the running CGI server scripts: # $web_server_cgi = "/var/www/cgi-bin/2d"; # path of the directory containing the map images and related docuemtns sub-directories in the server: # $web_server_html = "/var/www/html/2d"; # path for a directory to store temporary files in the server: # $web_server_html_tmp = "/var/www/html/2d/data/tmp"; # path for the small icons and logos in the server: # $web_server_icons = "/var/www/icons"; # name of the main script to query the database: # by default this name is "2d.cgi", but you can change it to any other value (e.g. nice2dpage.pl) # $web_server_main_script = "2d.cgi"; #-------------------------------------------------------------# #-------------------------------------------------------------# 1; #-------------------------------------------------------------# #-------------------------------------------------------------#