Set new paths, compatible with module

ProtoGene.pl

@@ -21,7 +21,7 @@ use LWP::Simple;                           # To test gigablaster availability
 use Mail::Send;                            # Send warnings and errors files by e-mail ==> only if the $userEMail variable is defined
 
 use lib '/mnt/common/share/ProtoGene/';    # Local path for ProtoGene's own perl modules
-use lib '/mnt/local/lib/tcoffee_perl/';
+#use lib '/mnt/local/lib/tcoffee_perl/';
 use Exonerate;                             # Exonerate runner, parser, ...
 use Views;                                 # Non-text outputs, e.g. HTML/CSS
 #use CheckOutput;                         # Check output for cds consistancy with query
@@ -29,9 +29,9 @@ use Views;                                 # Non-text outputs, e.g. HTML/CSS
 
 
 ################## CONFIGURATION ##################
-$ENV{'PATH'}        .= ':/mnt/local/bin/:./';                               # Additional path for executables
+#$ENV{'PATH'}        .= ':/mnt/local/bin/:./';                               # Additional path for executables
 
-my $cachePath        = '/scratch/cluster/monthly/t_coffee/ProtoGene_Cache'; # Cache directory
+my $cachePath        = '/scratch/fhgfs/tcoffee/ProtoGene_Cache';            # Cache directory
 my $cacheStorageTime = 15;                                                  # Do not update sequences younger than X days
 
 my $userEMail        = 'moretti.sebastien@gmail.com';                       # To receive e-mails with encountered problems; leave blank to inactive
@@ -58,8 +58,8 @@ my $blast_param = { 'evalue'    => 0.05,
 my $VERSION  = '4.1.0';
 
 my $webblast_exe  = '/mnt/common/share/ProtoGene/webblast.pl';
-my $blast_exe     = 'blastall';            # Or wu-blastall for Wu-BLAST; for local blast usage
-my $exonerate_exe = 'exonerate-1.0';       # Exonerate 1.0 because current parser only works with this version
+my $blast_exe     = 'blastall';        # Or wu-blastall for Wu-BLAST; for local blast usage
+my $exonerate_exe = 'exonerate';       # Exonerate 1.0 because current parser only works with this version
 
 
 ################## Option management

TODO

 - sort boj pos output
 
-- Exonerate 2+ ...
 - ssearch instead of blast to be more sensitive ?
 - add "respect case for seq name between in0 and in1"
 - add URL to help converting MSA/seq to fasta

runblast.pl

@@ -20,13 +20,13 @@ my $ret = GetOptions( 'p=s' => \$program,
                       'T=s' => \$html,);
 
 if( $program eq '' ){
-    &Usage();
+    Usage();
     exit(0);
 }
 
 
 my $dbtype = 'NucleotideDatabases';
-$dbtype    = 'ProteinDatabases' if( $program eq 'blastp' || $program eq 'blastx' );
+$dbtype    = 'ProteinDatabases'  if( $program eq 'blastp' || $program eq 'blastx' );
 
 
 if( $filter eq 'T' || $filter eq 'on' ){
@@ -36,7 +36,7 @@ else {
     $filter = 'off';
 }
 
-$html = 'on' if( $html eq 'T' );
+$html = 'on'  if( $html eq 'T' );
 
 
 
@@ -60,20 +60,20 @@ my $sequence = '';
 if ( $inputfile eq '' ){
     while( <STDIN> ){
         if( /^>/ ){
-            &RunBlast() if( $sequence ne '' );
+            RunBlast()  if( $sequence ne '' );
             $sequence = $_;
         }
         else {
             $sequence .= $_;
         }
     }
-    &RunBlast();
+    RunBlast();
 }
 elsif ( $inputfile ne ''){
-    open(INFILE,"$inputfile") if ( -e "$inputfile" );
+    open(INFILE,"$inputfile")  if ( -e "$inputfile" );
     while(<INFILE>){
         if( /^>/ ){
-            &RunBlast() if( $sequence ne '' );
+            RunBlast()  if( $sequence ne '' );
             $sequence = $_;
         }
         else {
@@ -82,10 +82,10 @@ elsif ( $inputfile ne ''){
         }
     }
     close INFILE;
-    &RunBlast();
+    RunBlast();
 }
 else{
-    &Usage();
+    Usage();
     exit(0);
 }
 

webblast.pl

@@ -16,9 +16,7 @@ use warnings;
 
 ############################  EXPRESSO PARAM  #################################################
 my $database_expresso  = 'pdb';                                   #PDB database name          #
-my $blast_dir_expresso = '/mnt/local/bin/blastall';               #blastall executable        #
-my $BLASTMAT           = 'export BLASTMAT=/mnt/local/ncbi/data/'; #matrix directory for blast #
-my $BLASTDB            = 'export BLASTDB=/db/blastnet/database/'; #PDB_seqres directoty       #
+my $blast_dir_expresso = 'blastall';                              #blastall executable        #
 ###############################################################################################
 
 my $runblast = 'runblast.pl';