Use FindBin

ProtoGene.pl

@@ -19,8 +19,8 @@ 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
 
-# TODO use FinBin for lib and binary paths !!!
-use lib '/software/SequenceAnalysis/ProtoGene/4.2.0/lib/'; # Local path for ProtoGene's own perl modules
+use FindBin qw( $RealBin );
+use lib "$RealBin/lib";                    # Local path for ProtoGene's own perl modules
 use Exonerate;                             # Exonerate runner, parser, ...
 use Views;                                 # Non-text outputs, e.g. HTML/CSS
 #use CheckOutput;                         # Check output for cds consistancy with query
@@ -54,14 +54,14 @@ my $blast_param = { 'evalue'    => 0.05,
 
 my $VERSION  = '4.2.2';
 
-my $webblast_exe  = '/software/SequenceAnalysis/ProtoGene/4.2.0/bin/webblast.pl';
+my $webblast_exe  = "$RealBin/utils/webblast.pl";
 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
 my ($msa, $revtrans, $pep, $hideBOJ, $run_name, $template, $lim) = ('', 0, 0, 0, '', '', 0);
-my ($cache, $cleancache)                                         = ('update', 'update');#TODO Finish to implement
+my ($cache, $cleancache)                                         = ('update', 'update'); #TODO Finish to implement
 my ($debug, $tmp)                                                = (0, 0);
 my ($db, $species, $local, $giga)                                = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0);
 my %opts = ('msa|in=s'        => \$msa,        # Input sequences