# Generated by SRI International Pathway Tools version 16.0 on Mon Apr 2, 2012 ################################################################################ # # Pathway Tools Init File # ----------------------- # This file contains initialization parameters for Pathway Tools. # Each parameter needs to be specified on its own line, with the name # of the parameter followed by a separator consisting of one or more space characters, # which are followed by the value, which is usually a text string or an integer. # # Lines beginning with the hash character "#" are ignored and are used for comments. # Therefore, when defining a value for a parameter whose line begins with "#", # please be sure to remove all hash characters from the line for that parameter # or it will remain inactive. # # The parameters in this file can usually be overridden by supplying the # corresponding command-line flags to the pathway-tools startup script. # ################################################################################ ################################################################################ # # Parameters for Pathway Tools when running in WWW server mode # -- Setting these parameters is MANDATORY if you run Pathway Tools in # WWW server mode. # Hostname of the machine on which Pathway Tools is running # WWW-Server-Hostname localhost # Port number on which Pathway Tools should listen for WWW server # requests, and which Pathway Tools will insert in URLs within the # WWW pages that it generates. The standard port for WWW servers is 80, # but this may require root privileges for starting up Pathway Tools. # WWW-Server-Port 1555 # The root directories of files (e.g., .html, .shtml, .js) served by # the server. You can specify one directory or a list of directories # separated by a '+' (no spaces). If a list, the directories will # be searched in the order given when serving static files. Do not # include a trailing slash or backslash at the end of the directories. # ###WWW-Html-Root-Dir /home/psgendb/local/pkg/biocyc_eco_shigella_install/aic-export/htdocs # Set this to "Y" (no quotes) if you would like gzip to apply compression on # CSS, HTML and JavaScript files served by the web server. # This will generate gzip compressed files in the same # directories as the original files, therefore enough # disk space and write access must be provided for these # directories to set this parameter to "Y". # The PATH variable must also have a path to gzip for this to work. # The default value for this parameter is "N". # The value "Y" is applicable only to non Microsoft Windows systems. # ###WWW-Use-Gzip N # Set this to "N" (no quotes) to disable the use of SVG to draw compounds and reactions. # SVG (Scalable Vector Graphics) is a web standard for drawing figures. # As of 16.0, Pathway Tools will use SVG on browsers that support it. # This parameter can turn off SVG, in which case the older style of graphics # will be used. # ###WWW-Use-SVG Y # Set this to "Y" (no quotes) to enable the web group feature. # The default value for this parameter is "N". # If web accounts database is set up, groups will be stored in the database # otherwise they will be stored in ptools-local/groups. NOTE: the first time # groups are turned on with a database, the schema will be upgraded, so PLEASE # make sure you make a backup first! # ###WWW-Enable-Groups N # Set this to "all" (no quotes) or a list of organism IDs, separated # by one or several '+' if several organism IDs, if you would like the # title of page objects to be the "Cyc" name of the database and not # the organism name. # If "all" is specified, it will apply to all databases. If a list of # organism IDs is given, it will only apply to these organisms. # The default value is "none". # ###Use-Cyc-Name none ################################################################################ # # Additional Parameters for Pathway Tools when running in WWW server mode # -- Setting these parameters is OPTIONAL if you run Pathway Tools in # WWW server mode. # The email address to which users of your Web site should send technical-support # email messages. This address will be inserted into pages generated on your Web site. # Please check to see whether test emails are being sent. If not, check # whether the executable /usr/lib/sendmail exists on the server machine, and whether # it is set up correctly to send messages. # ###Support-Email-Address biocyc-support@ai.sri.com # The name used for the Web site being operated by Pathway Tools. # This name will be inserted by Pathway Tools into pages that it generates # on your Web site. # ###WWW-Site-Name BioCyc # Specify which organisms should be published by the WWW server. # Users may publish all PGDBs on a site by using "all", # or a list of organism IDs delimited by +'s. # Example of the latter: ECOLI+META+VCHO # ###WWW-Publish all # Needed only for a Proxy WWW Server setup. # Port number on which another WWW server, such as Apache, will listen # for requests to forward them to the Pathway Tools WWW server. # When using this parameter, the other WWW server needs to be configured # to actually forward the requests. # ###WWW-Server-Proxy-Port 80 # If a WWW-Server-Port smaller than 1024 is specified, on UNIX, the root user # needs to start the Pathway Tools, and after the WWW server starts listening, # it will switch to the user account indicated here, to reduce security risks. # ###WWW-Server-User biocyc # Number of seconds after which Web pages expire, which were cached by the browser. # Setting this to a large value (like several days) should improve responsiveness for users, # because the static Web pages do not need to be reloaded from the Pathway Tools server. # Dynamically generated pages will however usually ignore this parameter. # ###WWW-Browser-Static-Page-Expiry-Seconds 604800 # If WWW-Quick-Search-Textfield-Label is set to a given string, then that string # will appear to the left of the Quick Search text box at the bottom of every # database page. The default is to have it say, "Quick Search". # To enter spaces into the string, use the underscore key: "Quick_Search". # ###WWW-Quick-Search-Textfield-Label Quick_Search # Set to "Y" to have the Query Page display the "Summary page for dataset" # link. A value of "N" suppresses it. # ###WWW-Show-Organism-Summary-Link Y # Set to "Y" to have the Query Page display the "History of updates for this # dataset" link. A value of "N" suppresses it. # ###WWW-Show-Update-History-Link Y # Set to "Y" to have the Query Page display the "Cellular Overview Diagram / # Omics Viewer" link. A value of "N" suppresses it. # ###WWW-Show-Diagram/Omics-Viewer-Links Y # Set to "Y" to have pathway displays include predicted enzymes by default. # A value of "N" means that only enzymes with experimental evidence will # appear unless the user requests to see all enzymes. # ###WWW-Default-Show-Predicted-Enzymes Y ################################################################################ # # Parameters used by Pathway Tools when accessing PGDBs within a MySQL # or Oracle server. # -- Setting these parameters is MANDATORY if you want to access PGDBs # from a MySQL or Oracle server. # Hostname of the machine on which the MySQL or Oracle PGDB server is running. # ###RDBMS-Server-Hostname # Port number on which either the MySQL or Oracle PGDB server is listening. # MySQL standard is 3306; Oracle standard is 1521 # ###RDBMS-Server-Port 3306 # Name of database within the MySQL or Oracle server in which PGDBs # should be stored. # ###RDBMS-Database-Name # Username used to log in to the MySQL or Oracle server. # If set to the value PROMPT, then the user will be prompted # for their username and password. # ###RDBMS-Username # Password used to log into the MySQL or Oracle server. # ###RDBMS-Password ################################################################################ # # Parameters used by Pathway Tools when accessing Ortholog-Links within a MySQL # server, for use with the Comparative Genome Browser. # -- Setting these parameters is MANDATORY only if you want to access # Ortholog-Links in a MySQL server. # Hostname of the machine on which the Ortholog-Link MySQL server is running. # ###Ortho-RDBMS-Server-Hostname # Port number on which the Ortholog-Link MySQL server is listening. # MySQL standard is 3306 # ###Ortho-RDBMS-Server-Port 3306 # Name of database within the MySQL server in which Ortholog-Links # should be stored. # ###Ortho-RDBMS-Database-Name # Username used to log in to the Ortholog-Link MySQL server. # ###Ortho-RDBMS-Username # Password used to log into the Ortholog-Link MySQL server. # ###Ortho-RDBMS-Password # Set to "Y" to obtain ortholog link data from SRI. # If you also configure the Ortho-RDBMS parameters above, both the defined RDBMS source above # and SRI will be used to obtain ortholog link data. # ###Get-Orthologs-From-SRI Y ################################################################################ # # Parameters for the Web Accounts system of Pathway Tools # when running in WWW server mode # -- Setting these parameters is OPTIONAL if you run Pathway Tools in # WWW server mode. # The Web Accounts system is used to manage logins, user profiles, and user preferences. # Hostname of the machine on which the MySQL Web Accounts server is running. If # commented out, then Web Accounts will be disabled for this Web server. # ###User-Account-RDBMS-Server-Hostname # Port number on which the MySQL Web Accounts server is listening. # MySQL standard is 3306 # ###User-Account-RDBMS-Server-Port 3306 # Name of database within the MySQL Web Accounts server in which user information # should be stored. # ###User-Account-RDBMS-Database-Name # Username used to log in to the MySQL Web Accounts server. # ###User-Account-RDBMS-Username # Password used to log into the MySQL Web Accounts server. # ###User-Account-RDBMS-Password # The ReCaptcha system is used by Web Accounts to authorize submissions by humans but block web-bots. # This is the ReCaptcha private key string tied to your server domain yourserver.com. # ###User-Account-ReCaptcha-private-key # This is the ReCaptcha public key string, also tied to your server domain yourserver.com. # You can get your own private and public keys for your domain for free from www.recaptcha.net. # ###User-Account-ReCaptcha-public-key ################################################################################ # # Parameters used by Pathway Tools when accessing Memos within a MySQL server. # -- Setting these parameters is MANDATORY only if you want to access # Memos in a MySQL server. # Hostname of the machine on which the Memos MySQL server is running. # ###Memos-RDBMS-Server-Hostname # Port number on which the MySQL Memos server is listening. # MySQL standard is 3306 # ###Memos-RDBMS-Server-Port 3306 # Name of database within the MySQL server, in which the Memos # should be stored. # ###Memos-RDBMS-Database-Name # Username used to log in to the Memos MySQL server. # ###Memos-RDBMS-Username # Password used to log into the Memos MySQL server. # ###Memos-RDBMS-Password ################################################################################ # # Parameters for sending email. # -- Setting these parameters is MANDATORY ONLY if you want Pathway Tools # to be able to send email. # # When running as a WWW server, Pathway Tools will allow users to report # bugs or communicate with users who create web accounts. To do this, it # must be configured to send email. # # Send email either through this machine's sendmail installation # or via an SMTP client that logs in to your site's SMTP server. # (Many sites that use IMAP or POP servers also require their users # to send mail by logging in to an SMTP server.) # # Choices are either "sendmail" (works with Unix/Macos only) or # "SMTP-Client" (works with either Unix/Macos or Windows). # If you can use your own local working sendmail installation then # no further configuration of email in this file is required. # If you use the SMTP-client method, then the parameters # beginning with "SMTP-" below must be set. # Email-Send-Method sendmail ################################################################################ # # Parameters for SMTP clients that log in to an SMTP server to send email. # -- Setting these parameters is MANDATORY ONLY if you chose the "SMTP-client" # setting for Email-Send-Method above. # Host providing mail service for this SMTP client. # ###SMTP-Host # Port for SMTP host. Standard is 25. # ###SMTP-Server-Port 25 # User name for login to SMTP server. # ###SMTP-Username # Password for login to SMTP server. # ###SMTP-Password # Use TLS for secure transport? # ###SMTP-TLS? NIL # Use SSL for secure transport? (note: setting this to true # will have priority over the SMTP-TLS? setting above and TLS # will not be used no matter how SMTP-TLS? is set.) # ###SMTP-SSL? NIL # # The following parameters are only used when SMTP-SSL? is set to true. # Most users will only need the first option, or the first two if using # a certificate for authentication. # For detailed information on the meaning of each option, see # http://www.franz.com/support/documentation/8.1/doc/operators/socket/make-ssl-client-stream.htm. # under the section "The keyword arguments". # SSL transport method, options are :sslv23 (default which will work with most servers), # :sslv2, :sslv3, :sslv3+ and :tlsvl. # ###SMTP-SSL-Method :sslv23 # Pathname to file containing certificate(s) for authentication to the SMTP server. # ###SMTP-SSL-Certificate # Pathname to the private key for the certificate, if not part of the certificate file. # ###SMTP-SSL-Key # Password for the SSL private key, if needed. # ###SMTP-SSL-Certificate-Password # Verify the certificate. Options are nil, :optional and :required. # ###SMTP-SSL-Verify nil # Max depth of certificate verification chain. # ###SMTP-SSL-MaxDepth 10 # File containing intermediate CA certificates for verifying certificate. # ###SMTP-SSL-CA-File # A directory containing a set of files, each with one intermediate CA file. # ###SMTP-SSL-CA-Directory # An OpenSSL cipher list. # ###SMTP-SSL-Ciphers