use CGI 'escape','img'; # here's the root of all our stuff $ROOT = '/perl/ace/elegans'; $WB = '/wormbase'; # The root is at the top level # ========= $NAME ========= # symbolic name of the database (defaults to name of file, lowercase) $NAME = 'elegans'; # ========= $HOST ========= # name of the host to connect to #$HOST = 'brie2.cshl.org'; #$HOST = 'stein.cshl.org'; $HOST = 'localhost'; #$HOST = 'brie.cshl.org'; # ========= $PORT ========= # Port number to connect to $PORT = 2005; # ========= $STYLESHEET ========= # stylesheet to use $STYLESHEET = "$WB/stylesheets/wormdb.css"; # ========= $PICTURES ========== # Where to write temporary picture files to: # The URL and the physical location, which must be writable # by the web server. @PICTURES = ('/ace_images' => '/var/tmp/ace_images'); # This controls at what point the "pic" script should stop making individually-clickable # elements. $MAX_IN_COLUMN = 100; # location of random pictures to display on certain pages $RANDOM_PICTS = "$WB/random_pic"; $PIC_SCRIPT = "$ROOT/misc/random_pic"; #========================= WORMBASE-SPECIFIC CONFIGURATION ================== # ========== An icon to use for "home" ========== # leaving this undefined suppresses the generation of a "home" link # $HOME_ICON = "$ICONS/arrows/uarrw.gif"; # ========= An icon to use for searching ======= # leaving this undefined suppresses the generation of a "search" link # $SEARCH_ICON = "$ICONS/unknown.gif"; # position of the big banner $BANNERS = "$WB/banners"; $BANNERS = "$WB/banners"; @BANNER_SIZE = (640,56); # fixed width for the page $PAGEWIDTH = 660; # position of the "cross" $CROSS_ICON = "$WB/images/cross1.gif"; $ARROWR_ICON = "$WB/images/arrow_right.gif"; $ARROWL_ICON = "$WB/images/arrow_left.gif"; # position of neuron diagrams $NEURON_DIAGRAMS = "$WB/cell/diagrams"; # ======== BLAST DATABASES =========== # location of BLAST databases $BLAST_ROOT = '/usr/local/wublast';; $BLAST_BIN = "$BLAST_ROOT/bin/"; $BLAST_MATRIX = "$BLAST_ROOT/matrix"; $BLAST_FILTER = "$BLAST_ROOT/filter"; $BLAST_DB = "/usr/local/acedb/elegans/blast"; $BLAST_CUTOFF = 0.001; $BLAST_MAXHITS = 20; @BLAST_default = ('blastp' => 'WormPep'); %BLAST_labels = ('EST_Elegans' => 'elegans ESTs', 'Elegans' => 'elegans genomic', 'WormPep' => 'WormPep'); %BLAST_ok = ('blastn' => [qw/Elegans EST_Elegans/], 'tblastn' => [qw/Elegans EST_Elegans/], 'blastp' => [qw/WormPep/], 'blastx' => [qw/WormPep/] ); # ========= $BANNER ========= # Banner HTML # This will appear at the top of each page. $BANNER = 'WormBase'; # ========= $FOOTER ========= # Footer HTML # This will appear at the bottom of each page # $FOOTER = img({-src=>"$WORMBASE/images/foot_logo.gif"}); $MY_FOOTER = a({-href=>'http://stein.cshl.org/'}, img({-border=>0,-src=>"$WB/images/foot_logo2.gif"}) ); # ========= @SEARCHES ========= # search scripts available # NOTE: the order is important @SEARCHES = ( basic => { name => 'Simple Search', url => "$ROOT/searches/basic", onimage => "$WB/buttons/basic_on.gif", offimage => "$WB/buttons/basic_off.gif", #width, height size => [109,20], }, expr_search => { name => 'Expr. Pattern Search', url => "$ROOT/searches/expr_search", onimage => "$WB/buttons/expr_on.gif", offimage => "$WB/buttons/expr_off.gif", size => [147,20], }, hunter => { name => 'Gene Hunter', url => "$ROOT/hunter/hunter.cgi", onimage => "$WB/buttons/hunter_on.gif", offimage => "$WB/buttons/hunter_off.gif", size => [100,20], }, # browser => { name => 'Class Browser', # url => "$ROOT/searches/browser", # onimage => "$WB/buttons/browser_on.gif", # offimage => "$WB/buttons/browser_off.gif", # size => [100,20], }, blast => { name => 'Blast Search', url => "$ROOT/searches/blast", onimage => "$WB/buttons/blast_on.gif", offimage => "$WB/buttons/blast_off.gif", size => [99,20], }, advanced => { name => 'Advanced Search', url => "$ROOT/searches/query", onimage => "$WB/buttons/advanced_on.gif", offimage => "$WB/buttons/advanced_off.gif", size => [129,20], }, atlas => { name => 'Worm Atlas', url => "$WB/atlas/atlas.html", onimage => "$WB/buttons/atlas_on.gif", offimage => "$WB/buttons/atlas_off.gif", size => [46,20], }, ); # ========= %HOME ========= # Home page URL @HOME = ( 'http://www.wormbase.org' => 'WormBase home' ); @HOME_BUTTON = ("$WB/buttons/home_bottom.gif" => [20,56]); # ========= %DISPLAYS ========= %DISPLAYS = ( gene => {'url' => "$ROOT/gene/locus", 'label' => 'Gene Report'}, cell => {'url' => "$ROOT/cell/cell.cgi", 'label' => 'Cell Summary'}, pedigree => {'url' => "$ROOT/cell/pedigree", 'label' => 'Pedigree Browser'}, mappingdata => {'url' => "$ROOT/gene/mapping_data", 'label' => 'Map Data'}, biblio => {'url' => "$ROOT/misc/biblio", 'label' => 'Bibliography'}, nearby_genes => {'url' =>"$ROOT/gene/genetable#pos", 'label' => 'Nearby Genes'}, geneapplet => {'url' =>"$ROOT/gene/geneapplet", 'label' => 'Interactive Map'}, hunter => {'url' =>"$ROOT/hunter/hunter.cgi", 'label' => 'Genome Hunter'}, sequence => { 'url' => "$ROOT/seq/sequence", 'label' => 'Sequence Report'}, author => { 'url' => "$ROOT/misc/author", 'label' => 'Author Info'}, biblio => {'url' => "$ROOT/misc/biblio", 'label' => 'Bibliography'}, clone => {'url' => "$ROOT/seq/clone", 'label' => 'Clone Report'}, paper => {'url' => "$ROOT/misc/paper", 'label' => 'Citation'}, laboratory => { 'url' => "$ROOT/misc/laboratory", 'label' => 'Lab Listing'}, expr_pattern => { 'url' => "$ROOT/gene/expression", 'label' => 'Expression Pattern'}, tree => { 'url' => "$ROOT/misc/etree", 'label' => 'Tree Display'}, xml => { 'url' => "$ROOT/misc/xml", 'label' => 'XML Dump'}, pic => { 'url' => "$ROOT/misc/epic", 'label' => 'Graphic Display'}, align => { 'url' => "$ROOT/seq/align", 'label' => 'alignment'}, ); # ========= %CLASSES ========= # displays to show %CLASSES = ( # There are three representations of Locus, in addition to the basic ones Locus => [ qw/gene mappingdata nearby_genes hunter biblio geneapplet/ ], # there are two representations of sequence, in addition to the basic ones Sequence => [ qw/sequence nearby_genes hunter/ ], # two representations of Author Author => [ qw/author biblio/ ], # one representation of Clone, Paper, Laboratory, and Expr_pattern Clone => [ 'clone' ], Paper => [ 'paper' ], Cell => [ 'cell','pedigree' ], Map => [ 'pic', 'geneapplet' ], Laboratory => [ 'laboratory' ], Expr_pattern => [ 'expr_pattern' ], # default has special meaning Default => [ qw/tree xml pic/ ], ); # ========= &URL_MAPPER ========= # mapping from object type to URL. Return empty list to fall through # to default. sub URL_MAPPER { my ($display,$name,$class) = @_; # Small Ace inconsistency: Models named "#name" should be # transduced to Models named "?name" $name = "?$1" if $class eq 'Model' && $name=~/^\#(.*)/; my $n = escape($name); my $c = escape($class); my $qs = "name=$n"; my $qsc = "name=$n&class=$c"; return (laboratory => $qs) if $class eq 'Laboratory'; return (paper => $qs) if $class eq 'Paper'; return (biblio => "$qs&class=Keyword") if $class eq 'Keyword'; return (clone => $qs ) if $class eq 'Clone'; return (gene => $qs ) if $class eq 'Locus'; return (sequence => $qs ) if $class eq 'Sequence'; return (expr_pattern => $qs) if $class eq 'Expr_pattern'; return (author => $qs ) if $class eq 'Author'; return (tree => $qsc) if $class eq 'Metabolite'; return (cell => $qs) if $class eq 'Cell'; if ($class eq 'Pathway') { return (pic => $qsc ) if $name =~ /^\*/; return (tree => $qsc) if $name !~ /^\*/; } # maps are always displayed graphically by default return (pic => $qsc ) if $class =~ /map/i; # pictures remain pictures return (pic => $qsc ) if $display eq 'pic'; return (tree => $qsc ); } # ========= Configuration information for the simple search script @SIMPLE = ('Any' => 'Anything', 'Accession_number' => 'Genbank Accession Number', 'Author' => 'Author', 'Cell' => 'Cell', 'Clone' => 'Clone', 'Locus' => 'Confirmed Gene', 'Genetic_map' => 'Genetic Map', 'Predicted_gene' => 'Predicted Gene', 'Sequence' => 'Sequence (any)', 'Genome_sequence', => 'Sequence (genomic)', 'Sequence_map' => 'Sequence Map', 'Strain' => 'Worm Strain', ); # Jalview configuration information $JALVIEW = '/applets/jalview.jar'; $JALVIEW_MAIL = 'beta.crbm.cnrs-mop.fr'; $JALVIEW_HELP = 'http://circinus.ebi.ac.uk:6543/jalview/help.html'; # Meow configuration $MEOW_CONFIRMED = 'http://iubio.bio.indiana.edu/meow/.bin/moquery?dbid=ACEDB:'; $MEOW_PREDICTED = 'http://iubio.bio.indiana.edu/meow/.bin/moquery?dbid=ACEPRED:'; # ========= Configuration information for the feedback script @FEEDBACK_RECIPIENTS = ( [ ' Paul Sternberg ' => 'general complaints and suggestions'=>1 ], [ ' Lincoln Stein ' => 'user interface' ], [ ' Norma Foltz ' => 'cells and expression patterns' ], [ ' Jonathan Hodgkin & Sylvia Martinelli ' => 'genetic data; gene names'], [ ' wormbase@caltech.edu ' => 'gene regulation and interactions' ], [ ' Sylvia Martinelli ' => 'addresses' ], [ ' Theresa Stiernagle ' => 'strains, bibliographic references' ], [ ' Richard Durbin ' =>'systematic genome sequence analysis, acedb problems' ], [ ' Danielle & Jean Thierry-Mieg ' => 'gene structures, ESTs and new largescale datasets' ], [ ' John Spieth ' => 'St. Louis sequence annotations; gene structures' ], [ ' worm@sanger.ac.uk' => 'Cambridge sequence annotations; gene structures' ], [ ' Alan Coulson ' => 'physical map' ], ); @FEEDBACK_CHECKED = (0); # number zero is paul # position of the chromosome tables, in URL space $CHROMOSOME_TABLES = "$WB/chromosomes"; $CHROMOSOME_TABLE_LENGTH = 2_000_000; # all-important copyright statement $COPYRIGHT = "$WB/copyright.html"; # ========= transcript script =========== # dimensions of the transcript picture shown in the sequence screen @TRANSCRIPT_DIMENSIONS = ($PAGEWIDTH,150); $TRANSCRIPT_HEIGHT = 10; # ======== geneapplet script ========== $JADEX_PORT = 2005; $JADEX_PATH = '/applets/jadex.jar'; $JADEX_IMAGE = "$WB/images/geneticMapApplet.gif"; # ======== promoter motif search script ========== $PROMOTER_DB = "$WB/chromosomes/promoters.db";