--- /dev/null
+package Jpred;
+
+=head1 NAME
+
+jpred.pm -- Jpred module to define all necessary global and environment variables
+
+=cut
+
+use warnings;
+use strict;
+
+BEGIN {
+ use Exporter;
+ our @ISA = ('Exporter');
+ our @EXPORT = qw(
+ $WEBSERVER
+ $WEBSERVERCGI
+ $SERVERROOT
+ $SRSSERVER
+ $CHKLOG
+ $RESULTS
+ $PDBLNK
+ $CSS
+ $IMAGES
+ $JNET
+ $TIMEOUT
+ $BATCHLIM
+ $DUNDEE
+ $JPREDUSER
+ $JPREDEMAIL
+ $MAILHOST
+ $JPREDROOT
+ $BINDIR
+ $LIBDIR
+ $JOBDIR
+ $PREFIX
+ $RESOURCE
+ $BLASTDB
+ $SWALL
+ $SWALLFILT
+ $PDB
+ $PDB_DAT
+ $JPREDHEAD
+ $JPREDFOOT
+ xsystem
+ setup_jpred_env
+ );
+ our @EXPORT_OK = @EXPORT;
+}
+
+# library path for Mail::CheckUser dependency for jpred_form.
+# for some reason doesn't work if in PERL5LIB
+use lib '/sw/lib/perl5.10.1/lib/perl5';
+
+# URIs
+#our $WEBSERVER = 'http://www.compbio.dundee.ac.uk/www-jpred';
+our $WEBSERVER = 'http://webserv1.cluster.lifesci.dundee.ac.uk:3209';
+our $WEBSERVERCGI = "$WEBSERVER/cgi-bin";
+
+#$SERVERROOT = "$WEBSERVER/~www-jpred";
+our $SERVERROOT = "$WEBSERVER";
+our $SRSSERVER = 'http://srs.ebi.ac.uk/srs6bin/cgi-bin';
+our $CHKLOG = "$WEBSERVERCGI/chklog?";
+our $RESULTS = "$SERVERROOT/results";
+our $PDBLNK = "http://www.ebi.ac.uk/pdbsum/";
+our $CSS = "$SERVERROOT/jpred.css";
+our $IMAGES = "$SERVERROOT/images";
+our $JNET = "$SERVERROOT/about.html#jnet";
+
+# This is the time (in seconds) the job is allowed to take
+our $TIMEOUT = 60 * 60; # now is 60mins
+our $BATCHLIM = 200;
+
+our $DUNDEE = "http://www.dundee.ac.uk";
+
+# e-mail details
+our $JPREDUSER = 'www-jpred';
+our $JPREDEMAIL = 'www-jpred@compbio.dundee.ac.uk';
+our $MAILHOST = 'smtp.lifesci.dundee.ac.uk'; # CC 19/05/06 - updated to current smtp host from weevil
+
+# Server paths
+#our $JPREDROOT = '/homes/www-jpred/live';
+#our $JPREDROOT = '/homes/www-jpred/devel';
+our $JPREDROOT = '/home/asherstnev/Projects/Jpred.project/jpred/branches/portable';
+
+# Directory for binaries either on the cluster or on the www server
+our $BINDIR = "$JPREDROOT/bin";
+
+# path to perl modules
+our $LIBDIR = "$JPREDROOT/lib";
+
+# Cluster paths
+our $JOBDIR = "$JPREDROOT/public_html/results"; # directory for output
+
+# Cluster names
+our $PREFIX = "jp_"; # Prefix for job submissions (qstat will only display 10 chars of job name)
+our $RESOURCE = "www_service2"; # Resource for the submission to use
+
+# Variables for external programs
+# psiblast
+$ENV{BLASTMAT} = "$JPREDROOT/data/blast";
+our $BLASTDB = $JPREDROOT . "/databases";
+$ENV{BLASTDB} = $BLASTDB;
+our $SWALL = "$BLASTDB/uniref90";
+our $SWALLFILT = "$SWALL.filt";
+our $PDB = '/db/blastdb/pdb';
+our $PDB_DAT = '/db/blastdb/DB.dat';
+
+# ncoils matrix location
+$ENV{COILSDIR} = "$JPREDROOT/data/coils";
+
+sub setup_jpred_env {
+ my $newJPREDROOT = shift;
+
+ $JPREDROOT = $newJPREDROOT if (defined $newJPREDROOT);
+
+ $BINDIR = "$JPREDROOT/bin";
+ $LIBDIR = "$JPREDROOT/lib";
+ $JOBDIR = "$JPREDROOT/public_html/results";
+
+ $ENV{BLASTMAT} = "$JPREDROOT/data/blast";
+ $BLASTDB = $JPREDROOT . "/databases";
+ $ENV{BLASTDB} = $BLASTDB;
+ $SWALL = "$BLASTDB/uniref90";
+ $SWALLFILT = "$SWALL.filt";
+}
+
+# Error checking system call
+sub xsystem {
+ my ($command) = @_;
+ my $rc = 0xffff & system $command;
+ if ( $rc == 0 ) {
+ return;
+ } elsif ( $rc == 0xff00 ) {
+ print "'$command' failed!\n";
+ die "Jpred failed\n";
+ } elsif ( ( $rc & 0xff ) == 0 ) {
+ $rc >>= 8;
+ die "'$command' did something else! (exited $rc)\n";
+ } else {
+ if ( $rc & 0x80 ) {
+ $rc &= ~0x80;
+ print "'$command' dumped core!\n";
+ die "Jpred failed\n";
+ }
+ }
+}
+
+# The header and footer for any HTML produced dynamically
+our $JPREDHEAD = " <div id=\"header\">
+
+ <a href=\"$DUNDEE\">
+ <img class=\"uod\" src=\"$IMAGES/logo_white_small.gif\" height=\"100\" width=\"108\" title=\"University of Dundee\" alt=\"University of Dundee Logo\" />
+ </a>
+ <a href=\"$SERVERROOT/index.html\">
+ <img src=\"$IMAGES/jpred3.png\" border=\"0\" height=\"102\" width=\"520\" title=\"Jpred Logo\" alt=\"Jpred Logo\" />
+ </a>
+ <a href=\"http://www.compbio.dundee.ac.uk\">
+ <img src=\"$IMAGES/group.png\" border=\"0\" height=\"102\" width=\"70\" title=\"Group Link\" alt=\"The Barton Group\" />
+ </a>
+
+ <div id=\"navigation\">
+ <table border=\"0\" cellpadding=\"0\" width=\"100%\">
+ <tr>
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/index.html\">Home</a></td>
+
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/about.html\">About</a></td>
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/new.html\">News</a></td>
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/faq.html\">FAQ</a></td>
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/help.html\">Help</a></td>
+ <td class=\"nav_table\"><a class=\"nav\" href=\"$SERVERROOT/contact.html\">Contact</a></td>
+ </tr>
+
+ </table>
+ </div> <!-- End #navigation -->
+ </div> <!-- End #header -->
+";
+
+our $JPREDFOOT = '
+ <script type="text/javascript">
+ var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+ document.write(unescape("%3Cscript src=\'" + gaJsHost + "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
+ </script>
+ <script type="text/javascript">
+ try{
+ var pageTracker = _gat._getTracker("UA-5356328-1");
+ pageTracker._trackPageview();
+ } catch(err) {}
+ </script>
+';
+1;
+
+=head1 DESCRIPTION
+
+This module defines all the global and envirnmental variables required by the Jpred server scripts and binaries.
+
+=head1 AUTHOR
+
+I'm not sure who originally wrote this module, but I guess all of the following contributed:
+
+James Cuff
+Jon Barber
+Chris Cole <christian@cole.name> (current maintainer)
+
+=cut
git://source.jalview.org / jabaws.git / blobdiff