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 $JPREDFOOT &xsystem);
- our @EXPORT_OK = @EXPORT;
+ use Exporter;
+ our @ISA = ('Exporter');
+ our @EXPORT =
+ qw($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);
+ 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://webservices.compbio.dundee.ac.uk:3209';
+#production server
+#our $WEBSERVER = 'http://www.compbio.dundee.ac.uk/www-jpred';
+#development server
+our $WEBSERVER = 'http://gjb-www-1.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";
+#our $SRSSERVER = 'http://srs.ebi.ac.uk/srs6bin/cgi-bin';
+our $SRSSERVER = 'http://www.ebi.ac.uk/ebisearch/search.ebi';
+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 $TIMEOUT = 60 * 60; # now is 60mins
our $BATCHLIM = 200;
our $DUNDEE = "http://www.dundee.ac.uk";
# e-mail details
-our $JPREDUSER = 'www-jpred';
+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
-
+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/live';
+our $JPREDROOT = '/homes/www-jpred/devel';
# Directory for binaries either on the cluster or on the www server
our $BINDIR = "$JPREDROOT/bin";
our $LIBDIR = "$JPREDROOT/lib";
# Cluster paths
-our $JOBDIR = "$JPREDROOT/public_html/results"; # directory for output
+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
+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";
+our $BLASTDB = $JPREDROOT . "/databases";
$ENV{BLASTDB} = $BLASTDB;
-our $SWALL = "$BLASTDB/uniref90";
+our $SWALL = "$BLASTDB/uniref90";
our $SWALLFILT = "$SWALL.filt";
-our $PDB = '/db/blastdb/pdb';
-our $PDB_DAT = '/db/blastdb/DB.dat';
+our $PDB = '/db/blastdb/pdb';
+our $PDB_DAT = '/db/blastdb/DB.dat';
# ncoils matrix location
$ENV{COILSDIR} = "$JPREDROOT/data/coils";
# 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";
- }
- }
+ 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