#########################
# MINE_Customization_File
########################
# THIS is like a small library - it returns "true" to the
# main scripts like a library, but it contains no functions or code,
# just a simple set of global
# variables that can be set to customize MINE

1;		# returns true to the main program

# THIS FILE IS CONSTANTLY EVOLVING
# NEWEST ADDITIONS
# $show_source
# $source_path

# USER PREFERENCES/CUSTOMIZATIONS


# CUSTOMIZATIONS THAT ARE NOT MADE IN THIS FILE
 
# 1) SECURITY
# To add security, you should limit the machines that can access the database with full permission
# to only a few IP addresses.  You can do this in the CGI-MINE.pl file in the function
# "CHECK PERMISSION"

# 2) PREFERENCES
# The submit, edit and search scripts (in the MINE menu)  use the file 
# MINE_PREFENCES to create their webforms.
# Use the instructions in the MINE_PREFENCES.default file to create your own 
# MINE_PREFERENCES file.
# If you use one of these scripts without editing this file you will get further
# instructions on how to do so (or see the MINE manual).


# PATH VARIABLES - UNDER CONSTRUCTION!
# Abs path to your source code files
# If you made source files with the ADMIN script
# you will need to manually mv or cp them to this
# directory to be able to view them from MINE
$source_path="http://www.wsu.edu/pseudomonas/cgi-bin/MINE/";

# paths for setting up the split of the data from the script...not yet implemented
# the default and log files go into the data directory

$AbsScripts = "/users/www/htdocs/pseudomonas/cgi-bin/MINE/";
$UrlScripts       = "http://www.wsu.edu/pseudomonas/cgi-bin/MINE/";
$AbsData     = "/users/www/htdocs/pseudomonas/cgi-bin/MINE/";
$UrlData          = "http://www.wsu.edu/pseudomonas/cgi-bin/MINE/";

# MINE MENU LINKS
$database_welcome_page = "\"http://www.wsu.edu/~mavrodi/q8r1.htm\"";
$database_name="Q8r1-96 Genome Database";
# COMMENT these lines out if you don't want links to PfSBW25 database on your menu - or fill them with your own webpages...
$database_link1 = "<a href= \"http://www.wsu.edu/~mavrodi/q8r1.htm\">List of Genes</a>";
$database_link2 = "<a href= \"http://www.wsu.edu/~mavrodi/contents.htm\">Index</a>";
$database_link3 = "<a href= \"http://www.wsu.edu/~mavrodi/Links.htm\">Related Links</a>";
$database_link4 = "<a href= \"http://www.wsu.edu/~mavrodi/lab_contact.html\">Contact Us</a>";

# BLAST 
        # This is the default name of the blast-database containing all
        # the .db files
        # blast-ready databases containing only subsets of files
        # can be prepared using the search engine
	$blast_database = "SELF_blast_database";  
# example "formatdb" command for preparing a blast database for blastall 
# see instructions for setting up this command to run as a cron job 
# $formatdb_cmd = "formatdb -i $blast_database -p F -o F";

# We found that the formatdb repeatedly failed when invoked through a CGI-script
#  - sometime it failed before all sequences have been included
# in the database.  To check if all sequences are there, look in the .nsq file that is created
# and see if all the headers are included.  
#  If you need to format a database manually use this:
# "formatdb -i $blast_database  -p F -o F" from the command line - this seems to
# always work
# The SELF_blast_database is reformated daily since it is entered into the crontab file of the
# manager.  Go to the MINE documentation to see how to do this:


####################################################################################
# RULES FOR USING FORMATDB  see the MINE manual for more details, or type formatdb on the
# command line if you have the blast suite of programs installed
####################################################################################
# A DNA database:
# formatdb -i ecoli.nt -p F -o T (the -o T is for indexing, many times will only work if OFF:
#              use -o -F instead)
#
# An AMINO ACID database:
# formatdb -i cat_yeast.faa -p T -o T
####################################################################################


# set this to 1 to show links to the source code at the bottom of each script
# set to 0 to hide these (for security or because you don't want to bother generating the
# copy of this source code as text files (go to ADMIN on the menu to make the actual source code files)
$show_source = 1;


# "EXTENSION" VARIABLES
# these are variables that define groups of files by pattern
# they are used to customize how file are shown to the viewer (e.g. Database Log)
# and how they are analyszed

# DATABASE LOG - "Page_Database_Log.cgi"
# list all the file extensions that you would like shown in the database log 
# (database log made 'on the fly' from this list)
@extensions = (
                "Q8.....db",
		"Q8.....db.fasta",
                "Pf5.....db",
		"Pf5.....db.fasta",
		"db_blastn.blast.html",
		"db_TblsatX.blast.html",
		"blast_database"
                );

# Augment the extensions above with descriptions
# This will also be shown in the database log
%extensions_labels = (
                "Q8.....db"=>"Q8r1-96 database files",
		"Pf5.....db"=>"Pf5 database files",
                "blast_database"=>"Concatenated fasta sequences generated by MINE from a subset of database sequences that is ready to use as a blast database"
                );


# DATABASE STATSITICS
# list the subset of the extensions used in the database that should have statistics generated
@stat_extensions = (
                "Q8.....db",
		"Pf5.....db"		
                );

# "SELF" BLAST DATABASE 
# list the subset of the extensions used in the database to be included in the "SELF_blast_database" file
# ($blast_database) in the "Page_Make_Source_ADMIN.cgi" script

@blast_extensions = (
                "Q8.....db",
		"Pf5.....db",
                );


# LINKING files in blast reports to their sources
# list the extensions of database entries so hyperlinks to the actual data files
# can be created inside all blast reports
         # e.g. $new_line =~ s/((Q8r1)([0-9]*)(.db))/<A HREF=\"$1\">$1<\/a>/g;
@link_extensions = (
                "Q8",
                "Pf5"
                );


# EXPERIMENTAL
# list the extension to be made into features in each fill to show the top blast hit
@top_blast_extensions = (
               "TblastX_GBK_Pf-dna.blast.html"
		);	


# "LINK_MINE" files are shown on in the display page: Page_LINK_MINE.cgi
# type "ls *LINK_MINE" to see what LINK_MINE file you have
# Feel free to create new ones!
# The 'hash' below is simple a chance to write a bit of description about each one of the
# LINE_MINE file you might create.
# A few already come with the MINE distribution to give you an idea..Here they are

%link_labels = (
	"Pseudomonas Blast Database Searches"=>"Links to Pseudomonas WWW blast servers",
	"Microbial Genomics-Proteomics"=>"(Mostly Meta-) Sites dedicated to storing and analyzing genome
	 and proteomes (all proteins)",
     	"Perl and Others"=>"Links to Perl resources (including a Perl Commands reference) some basic Javascript 
	 and Java, and HTML examples", 
     	"Software"=>"A list of bioinformatic tools and packages available that can be downloaded for free",
	"Essential"=>"Finding Essential (and generally helpful) things to help you understand 
	 and use the Internet like the best search engine (google.com)"
	); 


# (The last value at the end of the file must be true for this file to compile)