From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 6 Sep 2013 14:13:54 +0000 (+0100)
Subject: Fix problem with path to the UNIREF database
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=881afe63a8f476fdaff0cfc9f8ad4c790e4fd52b;p=jabaws.git

Fix problem with path to the UNIREF database
---

diff --git a/binaries/src/jpred/jpred.pl b/binaries/src/jpred/jpred.pl
index b7d02e7..74206dd 100755
--- a/binaries/src/jpred/jpred.pl
+++ b/binaries/src/jpred/jpred.pl
@@ -217,6 +217,11 @@ pod2usage( verbose => 2 ) if $man;
 
 #####################################################################################################
 # Key to database information and information for accessing them
+if (defined $jabaws) {
+  $db_path    = "/data/UNIREFdb";
+  $db_entry   = "cluster";
+}
+
 my $database = {
 
   ## default database used by Jpred
@@ -239,8 +244,8 @@ my $database = {
 
   ## cluster-specific path for Jpred
   cluster => {
-    database   => $db_path . "uniref90.filt",
-    unfiltered => $db_path . "uniref90",
+    database   => $db_path . "/uniref90.filt",
+    unfiltered => $db_path . "/uniref90",
   },
 
   ## these other DBs are experimental ones used during development.
@@ -264,9 +269,10 @@ my $database = {
   },
 };
 
-pod2usage(' ERROR! Input file with a sequence should be provided with  -sequence/-in')                           unless $infile;
-pod2usage(' ERROR! Unknown database at ' . $db_path . '. Use -dbpath and -dbname for configuring the database' ) unless exists $database->{$db_entry};
-pod2usage(' ERROR! UNIREF database doesn\'t exist. Use -dbpath and -dbname for configuring the database')        unless -f $database->{$db_entry}{database};
+my $dp = $database->{$db_entry}{database};
+pod2usage("ERROR! Input file with a sequence should be provided with -sequence/-in")                              unless $infile;
+pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database" )           unless exists $database->{$db_entry};
+pod2usage("ERROR! UNIREF database is not available at $dp. Use -dbpath and -dbname for configuring the database") unless -f $dp;
 
 if ( defined $prefix ) {
   unless (defined $outfile) {