Commit 9b94dd28 authored by Sebastien Carrere's avatar Sebastien Carrere

Bug iprscan defini mais vide. Cmd orthoMCL en tache de fond

parent 8529f45d
......@@ -258,15 +258,18 @@ sub ConfigureWorkdir
symlink(Cwd::abs_path($rh_analysis_params->{'proteomes'}->{$code}->{'fasta'}), "$WORKDIR/$code.fasta");
$rh_analysis_params->{'proteomes'}->{$code}->{'fasta'} = "$WORKDIR/$code.fasta";
if (defined $rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'})
if (defined $rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'} && -s $rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'})
{
symlink(Cwd::abs_path($rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'}), "$WORKDIR/$code.iprscan");
$rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'} = "$WORKDIR/$code.iprscan";
}
else
{
delete $rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'} if (defined $rh_analysis_params->{'proteomes'}->{$code}->{'iprscan'});
}
}
symlink(Cwd::abs_path($rh_analysis_params->{'orthomcl'}->{'outfile'}), "$WORKDIR/orthomcl.out")
if (defined $rh_analysis_params->{'orthomcl'}->{'outfile'} && -s $rh_analysis_params->{'orthomcl'}->{'outfile'});
symlink(Cwd::abs_path($rh_analysis_params->{'orthomcl'}->{'outfile'}), "$WORKDIR/orthomcl.out") if (defined $rh_analysis_params->{'orthomcl'}->{'outfile'} && -s $rh_analysis_params->{'orthomcl'}->{'outfile'});
return;
......
......@@ -210,13 +210,16 @@ sub ParseProteomes
foreach my $seqid (sort keys %h_fasta)
{
$h_species{$code}->{'sequences'}->{$seqid} = {};
$h_species{$code}->{'sequences'}->{$seqid}->{'sequence'} = $h_fasta{$seqid}->{'sequence'};
$h_species{$code}->{'sequences'}->{$seqid}->{'annotation'} = $h_fasta{$seqid}->{'header'};
$h_species{$code}->{'sequences'}->{$seqid}->{'iprscan'} = {};
$h_species{$code}->{'sequences'}->{$seqid}->{'iprscan'} = $rh_iprscan->{$seqid}
if (defined $rh_iprscan->{$seqid});
#CAS ORTHOMCL V2: LE CODE EST AUSSI DANS LE HEADER FASTA
my $clean_seqid = $seqid;
$clean_seqid =~ s/^$code\|// if ($clean_seqid =~ /^$code\|/);
$h_species{$code}->{'sequences'}->{$clean_seqid} = {};
$h_species{$code}->{'sequences'}->{$clean_seqid}->{'sequence'} = $h_fasta{$seqid}->{'sequence'};
$h_species{$code}->{'sequences'}->{$clean_seqid}->{'annotation'} = $h_fasta{$seqid}->{'header'};
$h_species{$code}->{'sequences'}->{$clean_seqid}->{'iprscan'} = {};
$h_species{$code}->{'sequences'}->{$clean_seqid}->{'iprscan'} = $rh_iprscan->{$seqid} if (defined $rh_iprscan->{$seqid});
$h_species{$code}->{'sequences'}->{$clean_seqid}->{'iprscan'} = $rh_iprscan->{$clean_seqid} if (defined $rh_iprscan->{$clean_seqid});
}
......
......@@ -42,7 +42,7 @@ sub LaunchAnalysis {
my $outdir = tempdir( CLEANUP => 0, DIR => $userdir );
#print STDERR "DEBUG $outdir :: $json_str\n";
print STDERR "DEBUG $outdir :: $json_str\n";
my $fh_json = &GetStreamOut("$outdir/analysis.json");
print $fh_json $json_str;
......@@ -50,9 +50,8 @@ sub LaunchAnalysis {
#print STDERR "DEBUG $outdir/analysis.json\n";
my $cmd =
"$FindBin::RealBin/../bin/int/bbric_orthomcl-companion.pl --verbose --outdir=$outdir --analysis_cfg=$outdir/analysis.json";
my $ret = system("(nohup $cmd > $outdir/log ) 2> $outdir/error");
my $cmd = "$FindBin::RealBin/../bin/int/bbric_orthomcl-companion.pl --verbose --outdir=$outdir --analysis_cfg=$outdir/analysis.json";
my $ret = system("(nohup $cmd > $outdir/log ) 2> $outdir/error&");
if ( $? == -1 ) {
%h_param = (
......
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