From 2cf032f4b987ba747c04159965aed78e3820d942 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 18 Nov 2013 14:38:54 +0000
Subject: [PATCH] JPRED-2 NEw version Jpred-3.0.2

---
 jpred/jpred        |    7 +++++--
 jpred/lib/Jpred.pm |    6 +++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/jpred/jpred b/jpred/jpred
index 6ed4104..30e9f40 100755
--- a/jpred/jpred
+++ b/jpred/jpred
@@ -79,13 +79,16 @@ Chris Cole <christian@cole.name> (current maintainer)
 
 use strict;
 use warnings;
-use Getopt::Long;
+use Getopt::Long qw(:config auto_version);
 use Pod::Usage;
 use Carp;
 use UNIVERSAL qw(isa);
 use Data::Dumper;
 use File::Temp;
 
+use FindBin qw($Bin);
+use lib "$Bin/../lib";
+
 use Jpred;  # needed to define BLAST environment variables
 
 # my modules
@@ -105,7 +108,7 @@ use Utils qw(profile);
 use Run qw(check);
 use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin);
 
-my $VERSION = '3.0.1';
+our $VERSION = '3.0.2';
 my $MAX_ALIGN = 1000;  # maximum number of alignment sequences allowed
 my $NR_CUT = 75;       # cut-off seqeunce ID value for defining non-redundancy
 
diff --git a/jpred/lib/Jpred.pm b/jpred/lib/Jpred.pm
index 6209621..a367d38 100755
--- a/jpred/lib/Jpred.pm
+++ b/jpred/lib/Jpred.pm
@@ -17,8 +17,8 @@ BEGIN {
 }
 
 # URIs
-our $WEBSERVER = 'http://www.compbio.dundee.ac.uk/www-jpred';
-#our $WEBSERVER = 'http://webservices.compbio.dundee.ac.uk:3209';
+#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";
@@ -43,7 +43,7 @@ our $MAILHOST = 'smtp.lifesci.dundee.ac.uk';   # CC 19/05/06 - updated to curren
 
 
 # Server paths
-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";
-- 
1.7.10.2