diff --git a/trunk/cfg/drap.cfg b/trunk/cfg/drap.cfg
index aa4062181b838d3c34302200211105f04750a7d2..03bfe458ec2cb9c01ec03ef6495e36ddfcda9d19 100644
--- a/trunk/cfg/drap.cfg
+++ b/trunk/cfg/drap.cfg
@@ -33,7 +33,6 @@ STAR
 tgicl
 TransDecoder.LongOrfs
 TransDecoder.Predict
-transrate
 trim_galore
 Trinity
 vecscreen
@@ -49,7 +48,6 @@ velvetg
 /usr/local/bioinfo/src/khmer/khmer2.0/khmerEnv/bin
 /usr/local/bioinfo/src/NCBI_Blast+/current/bin
 /usr/local/bioinfo/src/NCBI_tools/current/bin
-/usr/local/bioinfo/src/Transrate/current
 /usr/local/bioinfo/src/bwa/bwa-0.7.15
 
 [ENV] # Commands to execute to set the environnement (i.e. module load)
diff --git a/trunk/runAssessment b/trunk/runAssessment
index 4a991dd1cb3352f866ddb96c08bdb33e6dc45c70..9ee4ad05b283d0c04865b4ba2ed2f890823b9724 100755
--- a/trunk/runAssessment
+++ b/trunk/runAssessment
@@ -145,8 +145,9 @@ MAIN:
 		'busco_lineage' => "vertebrata_odb9",
 		'out_dir'       => "",
 		'binpath'       => $FindBin::RealBin."/bin",
+		'pluginspath'   => $FindBin::RealBin."/plugins",
 		'no_rate'       => 0,
-		'cfgfile'       => undef
+		'cfg-file'       => undef
 	};
 	
 	# Manage parameters
@@ -236,12 +237,14 @@ MAIN:
 			die "All your reads must be paired to use the scoring." ;
 		}
 	}
-	$opt->{out_dir} = File::Spec->rel2abs($opt->{out_dir});
-	$opt->{binpath} = File::Spec->rel2abs($opt->{binpath});
+	$opt->{out_dir}     = File::Spec->rel2abs($opt->{out_dir});
+	$opt->{binpath}     = File::Spec->rel2abs($opt->{binpath});
+	$opt->{pluginspath}	= File::Spec->rel2abs($opt->{pluginspath});
 
 	# Set softwares path
 	set_extended_path($config_file);
-	$ENV{PATH} = $FindBin::Bin."/bin:$ENV{PATH}" ;
+	$ENV{PATH} = join(':', glob("$opt->{pluginspath}/*")).":".$ENV{PATH};
+	$ENV{PATH} = $opt->{binpath}.":".$ENV{PATH} ;
 
 	# Set local mode
 	if ( defined($local) ){
@@ -271,7 +274,11 @@ sub process {
 	unless ($opt->{restart}) {
 		make_path($opt->{out_dir});
 	}
-	
+	# Write run command
+	open(LOG, ">>$opt->{out_dir}/workflow_cmd") or die "Can't open file $opt->{out_dir}/workflow_cmd\n";
+	print LOG $opt->{cmd}."\n";
+	close LOG;
+
 	# Init report
 	my $orig_report_folder = $opt->{binpath}."/../report" ;
 	my $report_folder = $opt->{out_dir}."/report" ;
@@ -470,7 +477,7 @@ sub get_ORF_analysis {
 			(
 				new Cmd( "cd ##STEP_DIR##" ),
 				new Cmd( "TransDecoder.LongOrfs -t ".$assembly ),
-				new Cmd( "TransDecoder.Predict -t ".$assembly ),
+				new Cmd( "TransDecoder.Predict --no_refine_starts -t ".$assembly ),
 				new Cmd( "cd -" )
 			)
 		);
diff --git a/trunk/runDrap b/trunk/runDrap
index 5b2c5f24a464e70736b191354df6c89c1cf482bb..d3ccb767ef6fab279e1f86eb2e4830c16ecd9fe8 100755
--- a/trunk/runDrap
+++ b/trunk/runDrap
@@ -57,7 +57,8 @@ my @getOptions = (
 	['cfg-file','s',undef,0],						# Allow user to define his own configuration file
 	['local',undef,undef,0],						# Execute jobs on local machine
 	['debug',undef,undef,0],						# run in debug mode
-	['no-qacct',undef,undef,0]						# no qacct request during assembly checking
+	['no-qacct',undef,undef,0],						# no qacct request during assembly checking
+	['no-check',undef,undef,0]						# no assembly checking
 );
 
 # defaults values
@@ -97,16 +98,17 @@ map { pod2usage("$_ is required") if ($required->{$_} && ! defined($opt->{$_}))
 map { my $key = $_; s/.+\|//; s/-/_/g; $opt->{$_} = delete($opt->{$key}) } keys %$opt;
 
 # initialize drap path
-$opt->{binpath}	   = "$FindBin::RealBin/bin";
-$opt->{cfgpath}	   = "$FindBin::RealBin/cfg";
-$opt->{reportpath} = "$FindBin::RealBin/report";
+$opt->{binpath}	    = "$FindBin::RealBin/bin";
+$opt->{cfgpath}	    = "$FindBin::RealBin/cfg";
+$opt->{pluginspath}	= "$FindBin::RealBin/plugins";
+$opt->{reportpath}  = "$FindBin::RealBin/report";
 
 ## allowing comma-separated lists of values as well as multiple occurrences of the options
 @{$opt->{R1}} = uniq(split(/,/, join(',', @{$opt->{R1}})));
 $opt->{pool} = scalar(@{$opt->{R1}});
 if (@{$opt->{R2}}) {
 	@{$opt->{R2}} = uniq(split(/,/, join(',', @{$opt->{R2}})));
-	printOutMessage("NUMBER of R1 and R2 FASTQ FILES DIFFERS") unless (scalar(@{$opt->{R1}}) == scalar(@{$opt->{R2}})); 
+	printOutMessage("NUMBER of UNIQ R1 and R2 FASTQ FILES DIFFERS") unless (scalar(@{$opt->{R1}}) == scalar(@{$opt->{R2}})); 
 }
 
 #------------------
@@ -217,6 +219,7 @@ if ($opt->{filter}) {
 }
 
 # create output directory
+$opt->{outdir} =~ s|/$||;
 mkdir($opt->{outdir}) or die "Can't create directory $opt->{outdir}\n" unless (-d $opt->{outdir});
 
 # add config params in %$opt
@@ -297,6 +300,7 @@ if (! $opt->{no_norm} && $opt->{norm_src} eq 'trinity' && (($opt->{norm} && $opt
 }
 
 # expand PATH and ENV variables
+$ENV{PATH} = join(':', glob("$opt->{pluginspath}/*")).":".$ENV{PATH};
 $ENV{PATH} = $opt->{binpath}.":".$ENV{PATH} ;
 set_extended_path($opt->{cfg_file});
 set_env_variables($opt->{cfg_file}, $opt);
@@ -424,7 +428,7 @@ Do not normalize reads before assembly.
 
 =item B<--norm-mem> INTEGER
 
-The maximum memory used for the normalization step in Gb of RAM. DRAP normalizes in two step if R1 (and R2)
+The maximum memory used for the normalization step in Gb of RAM. DRAP normalizes in two steps if R1 (and R2)
 parameter(s) are lists of fastq files: 1) DRAP normalizes each fastq file or pair of fastq files separately.
 2) DRAP merges normalized fastq files and performs another normalization on the merged fastq files or 
 pairs of fastq files.