Commit 5c7d5386 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Use FindBin

parent caade485
...@@ -19,8 +19,8 @@ use LWP::Simple; # To test gigablaster availability ...@@ -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 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 FindBin qw( $RealBin );
use lib '/software/SequenceAnalysis/ProtoGene/4.2.0/lib/'; # Local path for ProtoGene's own perl modules use lib "$RealBin/lib"; # Local path for ProtoGene's own perl modules
use Exonerate; # Exonerate runner, parser, ... use Exonerate; # Exonerate runner, parser, ...
use Views; # Non-text outputs, e.g. HTML/CSS use Views; # Non-text outputs, e.g. HTML/CSS
#use CheckOutput; # Check output for cds consistancy with query #use CheckOutput; # Check output for cds consistancy with query
...@@ -54,14 +54,14 @@ my $blast_param = { 'evalue' => 0.05, ...@@ -54,14 +54,14 @@ my $blast_param = { 'evalue' => 0.05,
my $VERSION = '4.2.2'; 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 $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 my $exonerate_exe = 'exonerate'; # Exonerate 1.0 because current parser only works with this version
################## Option management ################## Option management
my ($msa, $revtrans, $pep, $hideBOJ, $run_name, $template, $lim) = ('', 0, 0, 0, '', '', 0); my ($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, $tmp) = (0, 0); my ($debug, $tmp) = (0, 0);
my ($db, $species, $local, $giga) = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0); my ($db, $species, $local, $giga) = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0);
my %opts = ('msa|in=s' => \$msa, # Input sequences my %opts = ('msa|in=s' => \$msa, # Input sequences
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