diff --git a/tags/drap-v1.91/bin/AsmUtils.pm b/tags/drap-v1.91/bin/AsmUtils.pm
index f0d5cf3e8d98b22fb43e843236a3f8555fc7b3ba..1391c1905ef3e21f71ce9014794458277970fe42 100644
--- a/tags/drap-v1.91/bin/AsmUtils.pm
+++ b/tags/drap-v1.91/bin/AsmUtils.pm
@@ -177,7 +177,7 @@ sub print_msg {
 			delete $opt->{failed};
 		}
 		print " failed\n";
-		$opt->{display} = 0 unless ($opt->{step} eq 'reference'); # no need to print further msg if a step failed
+		$opt->{display} = 0 unless ($opt->{step} =~ /reference/); # no need to print further msg if a step failed
 	}
 }
 
@@ -492,6 +492,8 @@ sub rmbt_editing_complete {
 		foreach my $alignR1 (keys %{$opt->{rmbt_status}->{$opt->{rmbt_ref}->{"editing_$pass"}}}) {
 			$valid_rmbt++ if ($opt->{rmbt_status}->{$opt->{rmbt_ref}->{"editing_$pass"}}->{$alignR1}->{status} == 1);
 		}
+		return [0, 'empty', "$passes->{$pass}->[0]"] unless (-e "$passes->{$pass}->[0]");
+		return [0, 'empty', "$passes->{$pass}->[1]"] unless (-e "$passes->{$pass}->[1]");
 		my $nb_contigs_pre = count_inside_file($passes->{$pass}->[0], '^>');
 		my $nb_contigs_post = count_inside_file($passes->{$pass}->[1], '^>');
 		return [0, 1, $pass] unless ($valid_rmbt == scalar(@{$opt->{alignR1}}));
@@ -547,8 +549,8 @@ sub reference_complete {
 	my $log = get_more_recent_file("$opt->{outdir}/err_log", 'j10-*.o*');
 	my $err = get_more_recent_file("$opt->{outdir}/err_log", 'j10-*.e*');
 	my $run_dir = $opt->{tool} eq 'exonerate' ? 6 : 7;
-	my $run_cmd = get_more_recent_file("$opt->{dir_list}->[$run_dir]", "$opt->{tool}.*.sh");
-	return [0, 1, $run_cmd] if (-e $run_cmd); # runBlat and runExonerate clean sh, log and err files when all tasks ended successfully
+	my $tmp_dir = get_more_recent_dir("$opt->{dir_list}->[$run_dir]", "tmp_*");
+	return [0, 1, $tmp_dir] if (-e $tmp_dir); # runBlat and runExonerate cleans tmp dir when all tasks ended successfully
 	my $out_file = get_more_recent_file("$opt->{dir_list}->[$run_dir]", "*.$opt->{tool}.best.tsv");
 	return [0, 'empty', $out_file] unless (-e $out_file);
 	unless ($opt->{local}) {
@@ -673,8 +675,8 @@ sub meta_reference_complete {
 	my $log = get_more_recent_file("$opt->{outdir}/err_log", 'j10-*.o*');
 	my $err = get_more_recent_file("$opt->{outdir}/err_log", 'j10-*.e*');
 	my $run_dir = $opt->{tool} eq 'exonerate' ? 4 : 5;
-	my $run_cmd = get_more_recent_file("$opt->{dir_list}->[$run_dir]", "$opt->{tool}.*.sh");
-	return [0, 1, $run_cmd] if (-e $run_cmd); # runBlat and runExonerate clean sh, log and err files when all tasks ended successfully
+	my $tmp_dir = get_more_recent_dir("$opt->{dir_list}->[$run_dir]", "tmp_*");
+	return [0, 1, $tmp_dir] if (-e $tmp_dir); # runBlat and runExonerate cleans tmp dir when all tasks ended successfully
 	my $out_file = get_more_recent_file("$opt->{dir_list}->[$run_dir]", "*.$opt->{tool}.best.tsv");
 	return [0, 'empty', $out_file] unless (-e $out_file);
 	unless ($opt->{local}) {
diff --git a/tags/drap-v1.91/bin/LocalScheduler.pm b/tags/drap-v1.91/bin/LocalScheduler.pm
index 1ebc96d7b5c9735133c16bc1206510ad6ce5a123..781c73960f105f45b2b3b27d05899fc623a31fcc 100644
--- a/tags/drap-v1.91/bin/LocalScheduler.pm
+++ b/tags/drap-v1.91/bin/LocalScheduler.pm
@@ -100,7 +100,7 @@ sub parallel_submit {
 		$parallel_task = $available_cpu;
 	} else {
 		if ( $available_cpu < $cmdSet_max_cpu ){
-			$parallel_task = $available_cpu / ($cmdSet_max_cpu / scalar(@commands));
+			$parallel_task = int($available_cpu / ($cmdSet_max_cpu / scalar(@commands)));
 			if ( $parallel_task < 1 ) { $parallel_task = 1; }
 		}
 		else {
diff --git a/tags/drap-v1.91/bin/check_assembly.pl b/tags/drap-v1.91/bin/check_assembly.pl
index de8162615876ee5f6139b2db64bfd6bdc18e70a0..c9a59d531539814003e6bb572a625001ef66973e 100755
--- a/tags/drap-v1.91/bin/check_assembly.pl
+++ b/tags/drap-v1.91/bin/check_assembly.pl
@@ -73,7 +73,7 @@ my $msg = {
 		3 => "Can't find string 'COMPLETED: Processed .* mapped fragments...' inside SRC file",
 	},
 	'reference' => {
-		1 => "File SRC exists. All tasks did not ended successfully. Check err and log files inside reference directory",
+		1 => "Temporary directory SRC exists. All tasks did not ended successfully. Check err and log files inside reference directory",
 	},
 	'meta_rmbt' => {
 		1 => "The number of valid BAM files produced at the meta_rmbt step is not consistent with input data",
@@ -127,6 +127,7 @@ unless ($opt->{optimize}) {
 	}
 }
 print "Checking complete\n";
+set_drap_config($opt->{outdir}, $opt);
 exit 0;
 
 sub err_exit {
@@ -137,6 +138,7 @@ sub err_exit {
 	open(ERR, ">$err_file") or croak "Can't open file $err_file";
 	print ERR "$err_msg\n";
 	close ERR;
+	set_drap_config($opt->{outdir}, $opt);
 	exit 1;
 }
 
diff --git a/tags/drap-v1.91/bin/submitBlat.pl b/tags/drap-v1.91/bin/submitBlat.pl
index a7a2223591dabe6d4aa9c8fcc7f65c1f3c7f78c2..1e4e9321990e8583fcc5d5baf54adc4108e26946 100755
--- a/tags/drap-v1.91/bin/submitBlat.pl
+++ b/tags/drap-v1.91/bin/submitBlat.pl
@@ -312,7 +312,7 @@ MAIN:
 	my @out_files = scatter( \@in_files, "blat $target ##input## ".join(' ',@params).' ##output##', $scheduler, $mem, $vmem );
 	gather( \@out_files, $output );
 	`cat $output | blat_parser.pl > $best` if ($best);
-	exit;
+
 	# Remove temmporary files and folder
 	for( my $idx = 0 ; $idx < scalar(@in_files) ; $idx++ ){
 		unlink $in_files[$idx] ;
diff --git a/tags/drap-v1.91/bin/submitExonerate.pl b/tags/drap-v1.91/bin/submitExonerate.pl
index 898bb3d71ae2acc058dd9544158547501b55c6f0..80537432b506afd7c9d676d6c66fb47c141afaa0 100755
--- a/tags/drap-v1.91/bin/submitExonerate.pl
+++ b/tags/drap-v1.91/bin/submitExonerate.pl
@@ -134,8 +134,11 @@ sub gather {
 	}
 	foreach my $current_file ( @{$in_files} ){
 		open( my $FH_input, "cat $current_file | sort -k1,1 -k2,2rg |" ) or die "Cannot open ".$current_file ;
+		my @content = <$FH_input>;
+		close( $FH_input );
 		my $previous_id = "";
-		while( my @line = split(/\t/, <$FH_input>) ){
+		foreach ( @content ){
+			my @line = split(/\t/, $_);
 			$line[2] += 1;
 			if ($line[12] eq "-") {
 				my $tmp = $line[11];
diff --git a/tags/drap-v1.91/bin/write_jobs_files.pl b/tags/drap-v1.91/bin/write_jobs_files.pl
index a723d4c767ebd32b56bfadb83bcbdb5f9d52535e..843ce4293a84fb494ccf3e130ef87bad9e6c2428 100755
--- a/tags/drap-v1.91/bin/write_jobs_files.pl
+++ b/tags/drap-v1.91/bin/write_jobs_files.pl
@@ -68,6 +68,7 @@ unless (step_complete($opt)) {
 	my $local_restart = $opt->{restart};
 	if ($opt->{restart}) {
 		$clean_msg .= clean_directories($opt, 0);
+		$opt->{kmer_status}	= map { $_, 0 } @{$opt->{kmers}} if (ref($opt->{kmer_status}) eq 'HASH');
 		$opt->{restart} = 0;
 		$resubmit = $opt->{step};
 	}
@@ -616,9 +617,11 @@ unless (-f "$opt->{dir_list}->[4]/all_contigs.second_pass.fa" && step_complete($
 			              ."echo \$pending\nset pending_out = `eval \$pending`\necho \$pending_out\n"
 		}
 		$opt->{cmd} .= "samtools faidx $opt->{dir_list}->[3]/all_contigs.fa\n"
-		              ."set all_bams = `find $opt->{dir_list}->[4] -name \\*all_contigs.\\[0-9\\]\\*.bam`\nif (\"\$all_bams\" == '') exit\n"
-		              ."$opt->{binpath}/submitSamCorrectVar.pl --max-sub 70 --fasta $opt->{dir_list}->[3]/all_contigs.fa --bam \$all_bams --log $opt->{dir_list}->[4]/all_contigs.first_pass.raw.fa.samCorrectVariation.log --output $opt->{dir_list}->[4]/all_contigs.first_pass.raw.fa\n"
-		              ."cd-hit-est -i $opt->{dir_list}->[4]/all_contigs.first_pass.raw.fa -o $opt->{dir_list}->[4]/all_contigs.first_pass.fa -M 0 -d 0 -c 0.98 -T $opt->{env}->{n_cpu} > $opt->{dir_list}->[4]/all_contigs.first_pass.fa.cd-hit.log\n"
+		              ."set all_bams = `find $opt->{dir_list}->[4] -name \\*all_contigs.\\[0-9\\]\\*.bam`\nif (\"\$all_bams\" == '') exit\n";
+		$opt->{cmd} .= sprintf("%s/submitSamCorrectVar.pl --max-sub 70 --fasta %s/all_contigs.fa --bam \$all_bams --log %s/all_contigs.first_pass.raw.fa.samCorrectVariation.log --output %s/all_contigs.first_pass.raw.fa%s\n",
+			$opt->{binpath}, $opt->{dir_list}->[3], $opt->{dir_list}->[4], $opt->{dir_list}->[4], $opt->{local} ? ' --local' : ''
+		);
+		$opt->{cmd} .= "cd-hit-est -i $opt->{dir_list}->[4]/all_contigs.first_pass.raw.fa -o $opt->{dir_list}->[4]/all_contigs.first_pass.fa -M 0 -d 0 -c 0.98 -T $opt->{env}->{n_cpu} > $opt->{dir_list}->[4]/all_contigs.first_pass.fa.cd-hit.log\n"
 		              ."cat $opt->{dir_list}->[4]/all_contigs.first_pass.fa.clstr | ".q(perl -le '$/="\n>";map{s/^\d+.+>(\S+)\.\.\. \*$//m;$centroid=$1;print "$centroid\t$centroid";while(s/^\d+.+>(\S+)\.\.\..+//m){print "$1\t$centroid"}}<STDIN>')." > $opt->{dir_list}->[4]/all_contigs.first_pass.fa.cd-hit.history.log\n";
 		my $correctRef_metrics_file = $report_db_folder."/".$aln_edit_analysis->get_or_create_step('Correct consensus - first pass', 'Correct insertions, deletions and substitutions on contigs. It follow the majority vote at each position of the alignment.')->get_or_create_metrics_filename('correctVariationLog');
 		$opt->{cmd} .= "$opt->{binpath}/samCorrectVarMetrics2json.pl $opt->{dir_list}->[4]/all_contigs.first_pass.raw.fa.samCorrectVariation.log > $correctRef_metrics_file\n";
@@ -662,9 +665,11 @@ unless (-f "$opt->{dir_list}->[4]/all_contigs.second_pass.fa" && step_complete($
 		              ."echo \$pending\nset pending_out = `eval \$pending`\necho \$pending_out\n"
 	}
 	$opt->{cmd} .= "samtools faidx $opt->{dir_list}->[4]/all_contigs.first_pass.fa\n"
-	              ."set all_bams = `find $opt->{dir_list}->[4] -name \\*all_contigs.first_pass.\\[0-9\\]\\*.bam`\nif (\"\$all_bams\" == '') exit\n"
-	              ."$opt->{binpath}/submitSamCorrectVar.pl --max-sub 70 --fasta $opt->{dir_list}->[4]/all_contigs.first_pass.fa --bam \$all_bams --log $opt->{dir_list}->[4]/all_contigs.second_pass.raw.fa.samCorrectVariation.log --output $opt->{dir_list}->[4]/all_contigs.second_pass.raw.fa\n"
-	              ."cd-hit-est -i $opt->{dir_list}->[4]/all_contigs.second_pass.raw.fa -o $opt->{dir_list}->[4]/all_contigs.second_pass.fa -M 0 -d 0 -c 0.98 -T $opt->{env}->{n_cpu} > $opt->{dir_list}->[4]/all_contigs.second_pass.fa.cd-hit.log\n"
+	              ."set all_bams = `find $opt->{dir_list}->[4] -name \\*all_contigs.first_pass.\\[0-9\\]\\*.bam`\nif (\"\$all_bams\" == '') exit\n";
+	$opt->{cmd} .= sprintf("%s/submitSamCorrectVar.pl --max-sub 70 --fasta %s/all_contigs.first_pass.fa --bam \$all_bams --log %s/all_contigs.second_pass.raw.fa.samCorrectVariation.log --output %s/all_contigs.second_pass.raw.fa%s\n",
+		$opt->{binpath}, $opt->{dir_list}->[4], $opt->{dir_list}->[4], $opt->{dir_list}->[4], $opt->{local} ? ' --local' : ''
+	);
+	$opt->{cmd} .= "cd-hit-est -i $opt->{dir_list}->[4]/all_contigs.second_pass.raw.fa -o $opt->{dir_list}->[4]/all_contigs.second_pass.fa -M 0 -d 0 -c 0.98 -T $opt->{env}->{n_cpu} > $opt->{dir_list}->[4]/all_contigs.second_pass.fa.cd-hit.log\n"
 	              ."cat $opt->{dir_list}->[4]/all_contigs.second_pass.fa.clstr | ".q(perl -le '$/="\n>";map{s/^\d+.+>(\S+)\.\.\. \*$//m;$centroid=$1;print "$centroid\t$centroid";while(s/^\d+.+>(\S+)\.\.\..+//m){print "$1\t$centroid"}}<STDIN>')." > $opt->{dir_list}->[4]/all_contigs.second_pass.fa.cd-hit.history.log\n";
 	my $correctRef_metrics_file = $report_db_folder."/".$aln_edit_analysis->get_or_create_step('Correct consensus - second pass', 'Correct insertions, deletions and substitutions on contigs. It follow the majority vote at each position of the alignment.')->get_or_create_metrics_filename('correctVariationLog');
 	$opt->{cmd} .= "$opt->{binpath}/samCorrectVarMetrics2json.pl $opt->{dir_list}->[4]/all_contigs.second_pass.raw.fa.samCorrectVariation.log > $correctRef_metrics_file\n";
diff --git a/tags/drap-v1.91/doc/install.html b/tags/drap-v1.91/doc/install.html
index 66ae863a8f56c0c5c1098c9fc8b957a0e7c68b2a..95ebb9391456df844feb287157362e05e8b10c01 100644
--- a/tags/drap-v1.91/doc/install.html
+++ b/tags/drap-v1.91/doc/install.html
@@ -63,7 +63,7 @@
 			<pre class="prettyprint">docker create --name drap --privileged -v /mnt/scratch:/docker/scratch -i -t docker.io/sigenae/drap /bin/bash</pre>
 			<p>Start the Docker container and get bash into the running container.</p>
 			<pre class="prettyprint">docker start drap<br>docker exec -i -t drap /bin/bash</pre>
-			<p>The Docker container is configured to run with 120G of RAM and 8 CPU's.</p>
+			<p>The Docker container is configured to run with 120G of RAM and 6 CPU's.</p>
 			<p>DRAP is installed in the Docker container at '/usr/local/src/drap-v1.91'. Use that path as the INSTALL_FOLDER in the DRAP documentation.</p>
 			<div class="page-header">
 				<h1>Local install</h1>
@@ -86,6 +86,7 @@
 								<li>Bio::SeqIO</li>
 								<li>Bio::Tools::Run::StandAloneBlast</li>
 								<li>IPC::Run</li>
+								<li>List::Util</li>
 								<li>JSON</li>
 								<li>Term::ANSIColor</li>
 							</ul>
diff --git a/tags/drap-v1.91/doc/lib/src/Dockerfile b/tags/drap-v1.91/doc/lib/src/Dockerfile
index 55481cb16030189454a984341214b0fbe03a73cb..ed8f2dc746f87a53123f3a8a71633f4c5ac849ed 100644
--- a/tags/drap-v1.91/doc/lib/src/Dockerfile
+++ b/tags/drap-v1.91/doc/lib/src/Dockerfile
@@ -26,10 +26,10 @@ RUN apt-get update && apt-get install -y \
 	libgetopt-long-descriptive-perl \
 	libipc-run-perl  \
 	libjson-perl \
-	liblist-allutils-perl \
 	libncurses5-dev \
 	libpod2-base-perl \
 	libterm-extendedcolor-perl \
+	cpanminus \
 	make \
 	nano \
 	ncbi-blast+ \
@@ -39,16 +39,20 @@ RUN apt-get update && apt-get install -y \
 	python-biopython \
 	python-cutadapt \
 	python-scipy \
+	r-base \
+	r-cran-ggplot2 \
 	rna-star \
 	rssh \
 	ruby-dev \
-	samtools \
 	subversion \
 	transdecoder \
 	wget \
 	zlib1g-dev \
 && rm -rf /var/lib/apt/lists/*
 
+## -- Last version of List::Util Perl module -- ##
+RUN cpanm List::Util
+
 ## -- create links -- ##
 RUN cd /usr/bin \
 	&& ln -s $PWD/usr/bin/env /bin/env \
@@ -94,7 +98,7 @@ RUN cd /usr/local/src \
 	&& curl -SL http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz | tar -xz \
 	&& curl -SL http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz | tar -xz \
 	&& curl -SL http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz | tar -xz \
-	&& chmod +x BUSCO.py \
+	&& chmod +x BUSCO.py BUSCO_plot.py \
 	&& ln -s $PWD/BUSCO.py /usr/local/bin/BUSCO.py \
 	&& ln -s $PWD/BUSCO_plot.py /usr/local/bin/BUSCO_plot.py
 
@@ -129,12 +133,13 @@ ENV PERL5LIB /usr/local/src/tgicl_linux:$PERL5LIB
 
 ## -- install trinity -- ##
 RUN cd /usr/local/src \
-	&& curl -SL https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.3.2.tar.gz | tar -xz \
-	&& cd trinityrnaseq-Trinity-v2.3.2 \
+	&& curl -SL https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz | tar -xz \
+	&& cd trinityrnaseq-Trinity-v2.4.0 \
 	&& make && make plugins \
 	&& ln -s $PWD/Trinity /usr/local/bin/Trinity \
 	&& ln -s $PWD/util/insilico_read_normalization.pl /usr/local/bin/insilico_read_normalization.pl \
 	&& rm -rf $PWD/sample_data
+ENV PATH /usr/local/src/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/BIN:$PATH
 
 ## -- install transRate -- ##
 RUN cd /usr/local/src \
@@ -171,6 +176,6 @@ RUN cd /usr/local/src/drap-v1.91 \
 	&& sed -i -e 's|/path/to/contam_in_euks.fa|/usr/local/src/banks/contam_in_euks.fa|' cfg/drap.cfg \
 	&& sed -i -e 's|/path/to/mito.nt|/usr/local/src/banks/mito.nt|' cfg/drap.cfg \
 	&& sed -i -e 's|/path/to/busco_directory|/usr/local/src/busco|' cfg/drap.cfg \
+	&& sed -i -e 's|type = sge|type = local|' cfg/drap.cfg \
 	# correcting tgicl conflict version
-	&& sed -i -e 's/tgicl -F/tgicl/' bin/runAssembly.sh \
-	&& sed -i -e 's/s|TGICL_CPU|$opt->{env}->{n_cpu}|/s|TGICL_CPU|$opt->{env}->{n_cpu}-2|e/' bin/write_jobs_files.pl
+	&& sed -i -e 's/tgicl -F/tgicl/' bin/runAssembly.sh
diff --git a/tags/drap-v1.91/doc/quick_start.html b/tags/drap-v1.91/doc/quick_start.html
index 41e2dbf9c471d2e11ad5c4f43259ece09c30d50c..cf936b452cefa96bc923cc0733959d239444d40e 100644
--- a/tags/drap-v1.91/doc/quick_start.html
+++ b/tags/drap-v1.91/doc/quick_start.html
@@ -51,7 +51,7 @@
 		</div>
 		
 		<div class="content container theme-showcase" role="main">
-			<p>The following examples used two samples stored in <b>INSTALL_FOLDER</b>/test/data. SampleA and sampleB are two RNA-seq samples of fish embryos at different stages of development.</p>
+			<p>The following examples used two samples stored in <b>$INSTALL_FOLDER</b>/test/data. SampleA and sampleB are two RNA-seq samples of fish embryos at different stages of development.</p>
 			
 			<div class="page-header">
 				<h1>RunDrap</h1>
@@ -59,20 +59,20 @@
 			<div>
 				<p>This workflow is used to produce an assembly from one sample/tissue/development stage. In our example we need to launch runDrap on sampleA then on sampleB.</p>
 <pre class="prettyprint">
-<b>INSTALL_FOLDER</b>/runDrap \
- --R1 <b>INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz \
- --R2 <b>INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+<b>$INSTALL_FOLDER</b>/runDrap \
+ --R1 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz \
+ --R2 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
  --dbg oases -kmer 25,31,37,43,49 \
- --outdir <b>OUT_FOLDER</b>/oases_splA \
+ --outdir <b>$OUT_FOLDER</b>/oases_splA \
  --dbg-mem 16 --norm-mem 16
 
-<b>INSTALL_FOLDER</b>/runDrap \
- --R1 <b>INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
- --R2 <b>INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+<b>$INSTALL_FOLDER</b>/runDrap \
+ --R1 <b>$INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
+ --R2 <b>$INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
  --dbg oases --kmer 25,31,37,43,49 \
- --outdir <b>OUT_FOLDER</b>/oases_splB \
+ --outdir <b>$OUT_FOLDER</b>/oases_splB \
  --dbg-mem 16 --norm-mem 16
 </pre>
 			<p>Options <b>--dbg-mem</b> and <b>--norm-mem</b>  are not required for execution on cluster with SGE as scheduler (see <a href="install.html#configuration_file">drap.cfg</a>).
@@ -84,10 +84,10 @@
 			<div>
 				<p>This workflow is used to produce merge assemblies on several samples/tissues/development stages in one assembly without redundancy. In our example we merge information from two development stages.</p>
 <pre class="prettyprint">
-<b>INSTALL_FOLDER</b>/runMeta \
- --drap-dirs <b>OUT_FOLDER</b>/oases_splA,<b>OUT_FOLDER</b>/oases_splB \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
- --outdir <b>OUT_FOLDER</b>/meta_oases
+<b>$INSTALL_FOLDER</b>/runMeta \
+ --drap-dirs <b>$OUT_FOLDER</b>/oases_splA,<b>$OUT_FOLDER</b>/oases_splB \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+ --outdir <b>$OUT_FOLDER</b>/meta_oases
 </pre>
 			</div>
 
@@ -99,44 +99,44 @@
 				<h3>RunDrap and runMeta with trinity</h3>
 <pre class="prettyprint">
 # RunDrap with trinity on first development stage
-<b>INSTALL_FOLDER</b>/runDrap \
- --R1 <b>INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz \
- --R2 <b>INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+<b>$INSTALL_FOLDER</b>/runDrap \
+ --R1 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz \
+ --R2 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
  --dbg trinity \
- --outdir <b>OUT_FOLDER</b>/trinity_splA \
+ --outdir <b>$OUT_FOLDER</b>/trinity_splA \
  --dbg-mem 16 --norm-mem 16
 
 # RunDrap with trinity on second development stage
-<b>INSTALL_FOLDER</b>/runDrap \
- --R1 <b>INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
- --R2 <b>INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+<b>$INSTALL_FOLDER</b>/runDrap \
+ --R1 <b>$INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
+ --R2 <b>$INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
  --dbg trinity \
- --outdir <b>OUT_FOLDER</b>/trinity_splB \
+ --outdir <b>$OUT_FOLDER</b>/trinity_splB \
  --dbg-mem 16 --norm-mem 16
 </pre>
 				<p>Wait the end of the execution then launch runMeta.</p>
 <pre class="prettyprint">
 # RunMeta to merge DRAP trinity results
-<b>INSTALL_FOLDER</b>/runMeta \
- --drap-dirs <b>OUT_FOLDER</b>/trinity_splA,<b>OUT_FOLDER</b>/trinity_splB \
- --ref <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
- --outdir <b>OUT_FOLDER</b>/meta_trinity
+<b>$INSTALL_FOLDER</b>/runMeta \
+ --drap-dirs <b>$OUT_FOLDER</b>/trinity_splA,<b>$OUT_FOLDER</b>/trinity_splB \
+ --ref <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+ --outdir <b>$OUT_FOLDER</b>/meta_trinity
 </pre>
 				<h3>Comparison between assemblies</h3>
 <pre class="prettyprint">
 # Rename assemblies
-ln -s transcripts_fpkm_1.fa <b>OUT_FOLDER</b>/meta_oases/oases_fpkm_1.fa
-ln -s transcripts_fpkm_1.fa <b>OUT_FOLDER</b>/meta_trinity/trinity_fpkm_1.fa
+ln -s transcripts_fpkm_1.fa <b>$OUT_FOLDER</b>/meta_oases/oases_fpkm_1.fa
+ln -s transcripts_fpkm_1.fa <b>$OUT_FOLDER</b>/meta_trinity/trinity_fpkm_1.fa
 
 # Launch assessment
-<b>INSTALL_FOLDER</b>/runAssessment \
- --assemblies <b>OUT_FOLDER</b>/meta_oases/oases_fpkm_1.fa,<b>OUT_FOLDER</b>/meta_trinity/trinity_fpkm_1.fa \
- --R1 <b>INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz,<b>INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
- --R2 <b>INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz,<b>INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
- --protein-db <b>INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
- --outdir <b>OUT_FOLDER</b>/assessment
+<b>$INSTALL_FOLDER</b>/runAssessment \
+ --assemblies <b>$OUT_FOLDER</b>/meta_oases/oases_fpkm_1.fa,<b>$OUT_FOLDER</b>/meta_trinity/trinity_fpkm_1.fa \
+ --R1 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R1.fastq.gz,<b>$INSTALL_FOLDER</b>/test/data/sampleB_R1.fastq.gz \
+ --R2 <b>$INSTALL_FOLDER</b>/test/data/sampleA_R2.fastq.gz,<b>$INSTALL_FOLDER</b>/test/data/sampleB_R2.fastq.gz \
+ --protein-db <b>$INSTALL_FOLDER</b>/test/data/Danio_rerio.pep.fasta \
+ --outdir <b>$OUT_FOLDER</b>/assessment
 </pre>
 			</div>
 
diff --git a/tags/drap-v1.91/runDrap b/tags/drap-v1.91/runDrap
index cb2c4839e95f6838e47ee559af9c39667f583194..5b2c5f24a464e70736b191354df6c89c1cf482bb 100755
--- a/tags/drap-v1.91/runDrap
+++ b/tags/drap-v1.91/runDrap
@@ -6,6 +6,7 @@ use Getopt::Long;
 use FindBin;
 use File::Basename;
 use File::Spec;
+use List::Util qw(uniq);
 use POSIX qw(ceil);
 use lib("$FindBin::RealBin/bin");
 use AsmUtils;
@@ -101,10 +102,10 @@ $opt->{cfgpath}	   = "$FindBin::RealBin/cfg";
 $opt->{reportpath} = "$FindBin::RealBin/report";
 
 ## allowing comma-separated lists of values as well as multiple occurrences of the options
-@{$opt->{R1}} = split(/,/, join(',', @{$opt->{R1}}));
+@{$opt->{R1}} = uniq(split(/,/, join(',', @{$opt->{R1}})));
 $opt->{pool} = scalar(@{$opt->{R1}});
 if (@{$opt->{R2}}) {
-	@{$opt->{R2}} = split(/,/, join(',', @{$opt->{R2}}));
+	@{$opt->{R2}} = uniq(split(/,/, join(',', @{$opt->{R2}})));
 	printOutMessage("NUMBER of R1 and R2 FASTQ FILES DIFFERS") unless (scalar(@{$opt->{R1}}) == scalar(@{$opt->{R2}})); 
 }
 
@@ -173,7 +174,7 @@ if (@{$opt->{alignR1}}) {
 	printOutMessage("OPTIONS alignR1 AND alignTrim ARE MUTUALLY EXCLUSIVE'") if (defined($opt->{alignTrim}) && !$retrieve_conf);
 	printOutMessage("OPTIONS alignR1 AND alignNorm ARE MUTUALLY EXCLUSIVE'") if (defined($opt->{alignNorm}) && !$retrieve_conf);
 	printOutMessage("PLEASE GIVE alignR1 FASTQ FILE TO ALIGN")               if ($opt->{alignR1} eq "");
-	@{$opt->{alignR1}} = split(/,/, join(',', @{$opt->{alignR1}}));
+	@{$opt->{alignR1}} = uniq(split(/,/, join(',', @{$opt->{alignR1}})));
 	map { printOutMessage("NO SUCH FASTA FILE : $_") unless (-f $_) } @{$opt->{alignR1}};
 }
 
@@ -181,7 +182,7 @@ if (@{$opt->{alignR2}}) {
 	printOutMessage("OPTIONS alignR2 AND alignTrim ARE MUTUALLY EXCLUSIVE'") if (defined($opt->{alignTrim}) && !$retrieve_conf);
 	printOutMessage("OPTIONS alignR2 AND alignNorm ARE MUTUALLY EXCLUSIVE'") if (defined($opt->{alignNorm}) && !$retrieve_conf);
 	printOutMessage("PLEASE GIVE alignR2 FASTQ FILE TO ALIGN") if ($opt->{alignR2} eq "");
-	@{$opt->{alignR2}} = split(/,/, join(',', @{$opt->{alignR2}}));
+	@{$opt->{alignR2}} = uniq(split(/,/, join(',', @{$opt->{alignR2}})));
 	map { printOutMessage("NO SUCH FASTA FILE : $_") unless (-f $_) } @{$opt->{alignR2}};
 	printOutMessage("NUMBER of alignR1 and alignR2 FASTQ FILES DIFFERS") unless (scalar(@{$opt->{alignR1}}) == scalar(@{$opt->{alignR2}})); 
 }
diff --git a/trunk/bin/LocalScheduler.pm b/trunk/bin/LocalScheduler.pm
index 1ebc96d7b5c9735133c16bc1206510ad6ce5a123..781c73960f105f45b2b3b27d05899fc623a31fcc 100644
--- a/trunk/bin/LocalScheduler.pm
+++ b/trunk/bin/LocalScheduler.pm
@@ -100,7 +100,7 @@ sub parallel_submit {
 		$parallel_task = $available_cpu;
 	} else {
 		if ( $available_cpu < $cmdSet_max_cpu ){
-			$parallel_task = $available_cpu / ($cmdSet_max_cpu / scalar(@commands));
+			$parallel_task = int($available_cpu / ($cmdSet_max_cpu / scalar(@commands)));
 			if ( $parallel_task < 1 ) { $parallel_task = 1; }
 		}
 		else {