diff --git a/detectors/normalize/tools/buildSCDB.sh b/detectors/normalize/tools/buildSCDB.sh
index 3cfae96..3014eee 100755
--- a/detectors/normalize/tools/buildSCDB.sh
+++ b/detectors/normalize/tools/buildSCDB.sh
@@ -33,7 +33,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Building LSC coorientation graph..."
 		${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${ORG_LOGFILE} > LSC.tgf
 		${PROG_DIR}/cc.py LSC.tgf > LSC.cc
-		loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
+		loginfo " --> $($AwkCmd '{print $1}' LSC.cc | uniq | wc -l) connected componants"
 	loginfo "Done"
 
 
@@ -46,7 +46,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Extracting main connected components for LCS..."
 		rm -f LSC.direct.fasta
 		touch LSC.direct.fasta
-		for id in `awk '($1==0) {print $2}' LSC.cc`; do
+		for id in `$AwkCmd '($1==0) {print $2}' LSC.cc`; do
 			fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.direct.fasta
 		done
 		loginfo " --> $(fastaCount LSC.direct.fasta) sequences"
@@ -57,7 +57,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Extracting second connected components for LCS..."
 		rm -f LSC.reverse.fasta
 		touch LSC.reverse.fasta
-		for id in `awk '($1==1) {print $2}' LSC.cc`; do
+		for id in `$AwkCmd '($1==1) {print $2}' LSC.cc`; do
 			fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.reverse.fasta
 		done		
 		loginfo " --> $(fastaCount LSC.reverse.fasta) sequences"
@@ -75,7 +75,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Checking LCS homogeneity..."
 		${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${ORG_LOGFILE} > LSC_RefDB.tgf		
 		${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
-		NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
+		NCC=$($AwkCmd '{print $1}' LSC_RefDB.cc | uniq | wc -l)
 		if (( $NCC == 1 )); then
 			loginfo " --> $NCC connected componants"
 		else
@@ -105,7 +105,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Building SSC coorientation graph..."
 		${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${ORG_LOGFILE} > SSC.tgf
 		${PROG_DIR}/cc.py SSC.tgf > SSC.cc
-		loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
+		loginfo " --> $($AwkCmd '{print $1}' SSC.cc | uniq | wc -l) connected componants"
 	loginfo "Done"
 
 
@@ -119,7 +119,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Extracting main connected components for SSC..."
 		rm -f SSC.direct.fasta
 		touch SSC.direct.fasta
-		for id in `awk '($1==0) {print $2}' SSC.cc`; do
+		for id in `$AwkCmd '($1==0) {print $2}' SSC.cc`; do
 			fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.direct.fasta
 		done
 		loginfo " --> $(fastaCount SSC.direct.fasta) sequences"
@@ -130,7 +130,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Extracting second connected components for SSC..."
 		rm -f SSC.reverse.fasta
 		touch SSC.reverse.fasta
-		for id in `awk '($1==1) {print $2}' SSC.cc`; do
+		for id in `$AwkCmd '($1==1) {print $2}' SSC.cc`; do
 			fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.reverse.fasta
 		done		
 		loginfo " --> $(fastaCount SSC.reverse.fasta) sequences"
@@ -148,7 +148,7 @@ pushTmpDir ORG.buildSCDB
 	loginfo "Checking SSC homogeneity..."
 		${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${ORG_LOGFILE} > SSC_RefDB.tgf		
 		${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
-		NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
+		NCC=$($AwkCmd '{print $1}' SSC_RefDB.cc | uniq | wc -l)
 		if (( $NCC == 1 )); then
 			loginfo " --> $NCC connected componants"
 		else
diff --git a/detectors/normalize/tools/coorienteSC.sh b/detectors/normalize/tools/coorienteSC.sh
index ed6cc50..af4f38a 100755
--- a/detectors/normalize/tools/coorienteSC.sh
+++ b/detectors/normalize/tools/coorienteSC.sh
@@ -43,7 +43,7 @@ pushTmpDir  ORG.coorienteSC
 	
 	loginfo "Running Blast..."
 		blastn -db "${BLASTDB}" -query "${DATA}" -outfmt 6 | \
-	 	awk ' \
+	 	$AwkCmd ' \
 	 	      ($4 > 1000) && ($3 > 70) \
 	 	      ($1==QUERY) && \
 	 	      ($2==SUBJECT) && \
@@ -65,7 +65,7 @@ pushTmpDir  ORG.coorienteSC
 	 	                                         LDIFF= ($3/100.*$4) }} \
 	 	                                     } \
 	          END {print QUERY,SUBJECT,LSAME,LDIFF,(LSAME>LDIFF)}' | \
-     	awk -v minlength="${MINLENGTH}" \
+     	$AwkCmd -v minlength="${MINLENGTH}" \
      		  ' (($3>minlength) || \
        			($4 > minlength)) && \
        			($3/($4+1) > 2) && \
@@ -75,7 +75,7 @@ pushTmpDir  ORG.coorienteSC
                              {print $1,$2,$5}}' | \
         sort | \
         uniq -c | \
-        awk '($1==2) {print $2,$3,$4}'
+        $AwkCmd '($1==2) {print $2,$3,$4}'
 	loginfo "Done"
 	          
 popTmpDir
diff --git a/detectors/normalize/tools/extract_refLSC.sh b/detectors/normalize/tools/extract_refLSC.sh
index 55bbcab..7930655 100755
--- a/detectors/normalize/tools/extract_refLSC.sh
+++ b/detectors/normalize/tools/extract_refLSC.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                     \
diff --git a/detectors/normalize/tools/extract_refSSC.sh b/detectors/normalize/tools/extract_refSSC.sh
index 36660c6..e21d0e6 100755
--- a/detectors/normalize/tools/extract_refSSC.sh
+++ b/detectors/normalize/tools/extract_refSSC.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                     \
diff --git a/detectors/normalize/tools/selectViridiplantae.sh b/detectors/normalize/tools/selectViridiplantae.sh
index 25e644e..895dd06 100755
--- a/detectors/normalize/tools/selectViridiplantae.sh
+++ b/detectors/normalize/tools/selectViridiplantae.sh
@@ -2,7 +2,7 @@
 
 grep -A 1 '  ORGANISM' $* | \
   grep -B 1 Viridiplantae | \
-  awk '{print $1}' | \
+  gawk '{print $1}' | \
   grep '\.gbk' | \
   sed -E 's/(^.*\.gbk).$/\1/' | \
   uniq
\ No newline at end of file
diff --git a/detectors/rrna/bin/go_rrna.sh b/detectors/rrna/bin/go_rrna.sh
index 4d79957..d987cb9 100755
--- a/detectors/rrna/bin/go_rrna.sh
+++ b/detectors/rrna/bin/go_rrna.sh
@@ -33,13 +33,13 @@ pushTmpDir ORG.rrna
 	RRNA=$(basename ${QUERY})
 	
 	hmmsearch --max ${RRNADB} ${QUERY} | \
-		awk '/Query: / { \
+		$AwkCmd '/Query: / { \
 		                profil=$2; \
 		                match($3,"[0-9][0-9]*");\
 		                lprof=substr($3,RSTART,RLENGTH)} \
 		     / [0-9][0-9]* ! / { \
 		                print profil,lprof,$7,$8,$10,$11}' | \
-		awk '($3 <=5) && (($2-$4) <=5) { \
+		$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
 		                full=1;$5=$5-$3+1;$6=$6+($2-$4)}  
 		               {loc=$5".."$6} \
 		     ($1 ~ /_RC$/) { \
diff --git a/detectors/rrna/tools/buildRRNAModels.sh b/detectors/rrna/tools/buildRRNAModels.sh
index 8a9561f..fdb3c55 100755
--- a/detectors/rrna/tools/buildRRNAModels.sh
+++ b/detectors/rrna/tools/buildRRNAModels.sh
@@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 function fasta1li {
 
-    awk '/^>/ {if (sequence) \
+    $AwkCmd '/^>/ {if (sequence) \
                   {print sequence}; \
                print $0; \
                sequence=""} \
@@ -28,7 +28,7 @@ function dereplicate {
 		grep -v -- -- | \
 		sed -E "s/count=[0-9]+; //" | \
 		sed 's/cluster_weight/count/' | \
-		awk ' /^>/ {SEQ++;\
+		$AwkCmd ' /^>/ {SEQ++;\
 		            match($0,"count=[0-9][0-9]*;");\
 		            count=substr($0,RSTART,RLENGTH);\
 		            $1=$1"_"SEQ;\
@@ -58,7 +58,7 @@ function clustering {
 }
 
 function revcomp {
-    awk 'function printfasta(seq) {                                  \
+    $AwkCmd 'function printfasta(seq) {                                  \
             seqlen=length(seq);                                       \
             for (i=1; i <= seqlen; i+=60)                              \
               print substr(seq,i,60);                                 \
diff --git a/detectors/rrna/tools/extract_ref16S.sh b/detectors/rrna/tools/extract_ref16S.sh
index 1337eef..86b93a3 100755
--- a/detectors/rrna/tools/extract_ref16S.sh
+++ b/detectors/rrna/tools/extract_ref16S.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                    \
diff --git a/detectors/rrna/tools/extract_ref23S.sh b/detectors/rrna/tools/extract_ref23S.sh
index 31758c7..fc210df 100755
--- a/detectors/rrna/tools/extract_ref23S.sh
+++ b/detectors/rrna/tools/extract_ref23S.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                     \
diff --git a/detectors/rrna/tools/extract_ref4.5S.sh b/detectors/rrna/tools/extract_ref4.5S.sh
index 6f59c29..35c2ba5 100755
--- a/detectors/rrna/tools/extract_ref4.5S.sh
+++ b/detectors/rrna/tools/extract_ref4.5S.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                     \
diff --git a/detectors/rrna/tools/extract_ref5S.sh b/detectors/rrna/tools/extract_ref5S.sh
index bc90277..322227b 100755
--- a/detectors/rrna/tools/extract_ref5S.sh
+++ b/detectors/rrna/tools/extract_ref5S.sh
@@ -2,7 +2,7 @@
 #
 
 
-  awk 'function printfasta(seq) {                                            \
+  gawk 'function printfasta(seq) {                                            \
              seqlen=length(seq);                                             \
              for (i=1; i <= seqlen; i+=60)                                   \
                  print substr(seq,i,60);                                     \
diff --git a/detectors/rrna/tools/revcomp_alignments.sh b/detectors/rrna/tools/revcomp_alignments.sh
index e06a015..7d1d089 100644
--- a/detectors/rrna/tools/revcomp_alignments.sh
+++ b/detectors/rrna/tools/revcomp_alignments.sh
@@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 
 function revcomp {
-    awk 'function printfasta(seq) {                                  \
+    gawk 'function printfasta(seq) {                                  \
             seqlen=length(seq);                                       \
             for (i=1; i <= seqlen; i+=60)                              \
               print substr(seq,i,60);                                 \
diff --git a/detectors/trna/lib/aragorn_wrapper.awk b/detectors/trna/lib/aragorn_wrapper.awk
index 6fdcba9..83b6a48 100755
--- a/detectors/trna/lib/aragorn_wrapper.awk
+++ b/detectors/trna/lib/aragorn_wrapper.awk
@@ -1,4 +1,4 @@
-#!/usr/bin/awk -f
+#!/usr/bin/env gawk -f
 function genomeid() {
   if (gid=="") {
     gid="XXXXXXX";
diff --git a/detectors/trna/tools/buildCAURefDB.sh b/detectors/trna/tools/buildCAURefDB.sh
index a0de820..c97c89e 100755
--- a/detectors/trna/tools/buildCAURefDB.sh
+++ b/detectors/trna/tools/buildCAURefDB.sh
@@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 function fasta1li {
 
-    awk '/^>/ {if (sequence) \
+    $AwkCmd '/^>/ {if (sequence) \
                   {print sequence}; \
                print $0; \
                sequence=""} \
@@ -28,7 +28,7 @@ function dereplicate {
 		grep -v -- -- | \
 		sed -E "s/count=[0-9]+; //" | \
 		sed 's/cluster_weight/count/' | \
-		awk ' /^>/ {SEQ++;$1=$1"_"SEQ;print $0} \
+		$AwkCmd ' /^>/ {SEQ++;$1=$1"_"SEQ;print $0} \
 			 !/^>/ {print $0}'
 }
 
@@ -52,15 +52,16 @@ function goodtrna {
 	sumatra -t 0.90 -x $QUERY $REF | \
 		sed -E 's/.(trn.M?)[_A-Z0-9]+/ \1 /' | \
 		sort -k 1,2 | \
-		awk '(OLD) && ($1!=OLD) {print OLD,c["trnM"],c["trnfM"],c["trnI"]} \
+		$AwkCmd '(OLD) && ($1!=OLD) {print OLD,c["trnM"],c["trnfM"],c["trnI"]} \
 		     (OLD !=$1)         {c["trnM"]=0;c["trnfM"]=0;c["trnI"]=0;OLD=$1} \
-		                        {c[$2]+=$5}' | awk '{p=0;} \
+		                        {c[$2]+=$5}' | \
+		$AwkCmd '{p=0;} \
 		     ($2 > $3) && ($2 > $4) { print $0,"trnM";p=1 } \
 		     ($3 > $2) && ($3 > $4) {print $0,"trnfM";p=1} \
 		     ($4 > $2) && ($4 > $3) {print $0,"trnI";p=1} \
 		     (p==0) {print $0,"----"}' |      sed 's/_/ /' | \
-		awk '{print $1"_"$2,$3,$4,$5,$1,$6}' | \
-		awk '(($2+$3+$4) > 1) && ($5==$6) {print $1}'
+		$AwkCmd '{print $1"_"$2,$3,$4,$5,$1,$6}' | \
+		$AwkCmd '(($2+$3+$4) > 1) && ($5==$6) {print $1}'
 }
 
 pushTmpDir ORG.buildSCDB
diff --git a/detectors/trna/tools/extract_refCAUtRNA.sh b/detectors/trna/tools/extract_refCAUtRNA.sh
index 6a8866e..f71f1e1 100755
--- a/detectors/trna/tools/extract_refCAUtRNA.sh
+++ b/detectors/trna/tools/extract_refCAUtRNA.sh
@@ -15,11 +15,11 @@ function taxid {
 }
 
 function ac {
-	head -1 $1 | awk '{print $2}'
+	head -1 $1 | $AwkCmd '{print $2}'
 }
 
 function definition {
-	awk '/^DEFINITION/      {on=1}                         \
+	$AwkCmd '/^DEFINITION/      {on=1}                         \
 	     (on==1)            {printf("%s ",$0)}             \
 	     (/\.$/ && (on==1)) {on=0;print ""}' $1 |          \
 	sed 's/^DEFINITION *//' | \
@@ -33,7 +33,7 @@ function gb2fasta {
 
     echo ">${AC} taxid=${TAXID}; ${DEFINITION}"
     
-    awk '/^\/\//    {on=0}                                             \
+    $AwkCmd '/^\/\//    {on=0}                                             \
          (on==1)    {print $0}                                         \
          /^ORIGIN / {on=1}' $1 |                                       \
     sed -E 's/^ *[0-9]+ +//'   |                                       \
@@ -46,11 +46,11 @@ function findCAUtrna {
 
 	gb2fasta $1 > ${FASTATMP}
 	aragorn -i -w -seq ${FASTATMP} |                               \
-	awk '(on==1) && /^ *[0-9]+/ {on=0;print ""}                       \
+	$AwkCmd '(on==1) && /^ *[0-9]+/ {on=0;print ""}                       \
 	     (on==1)                {printf($0)}                          \
 	     /\(cat\)$/             {on=1; printf("%s ",$0)}              \
 	     END {print ""}' | \
-	awk '{print $3,$6}'  | \
+	$AwkCmd '{print $3,$6}'  | \
 	sed -E 's/c?\[([0-9]+),([0-9]+)\]/\1 \2/' | \
 	sed 's/ /:/g'
 	
@@ -58,10 +58,10 @@ function findCAUtrna {
 }
 
 function trnaAnnotations {
-    awk '/^ORIGIN/    {on=0} \
+    $AwkCmd '/^ORIGIN/    {on=0} \
          (on==1)      {print $0} \
          /^FEATURE/   {on=1}' $1 | \
-    awk '/^     [^ ]/ {print ""} \
+    $AwkCmd '/^     [^ ]/ {print ""} \
                       {printf("%s ",$0)} \
          END          {print ""}' | \
     sed 's/^ *//' | \
@@ -76,17 +76,17 @@ function trnaAnnotations {
     sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
     sed 's/^tRNA *//' |  \
     sed -E 's@([0-9]+) +([0-9]+).*/gene="([^"]+)"@\1 \2 \3@' | \
-    awk '{print $1,$2,$3}' 
+    $AwkCmd '{print $1,$2,$3}' 
 }
 
 function annotateCAU {
     DISTTMP="$$.trna.dist"
 	trna=(`echo $1 | sed 's/:/ /g'`) 
-	awk -v b=${trna[0]} -v e=${trna[1]} \
+	$AwkCmd -v b=${trna[0]} -v e=${trna[1]} \
 	    '{printf("sqrt((%d - %d)^2 + (%d - %d)^2)\n",$1,b,$2,e)}' $2 | \
 	bc -l | \
 	sed 's/\..*$//' > ${DISTTMP}
-	paste ${DISTTMP} $2 | sort -nk 1 | head -1 | awk '{print $1,$4}'
+	paste ${DISTTMP} $2 | sort -nk 1 | head -1 | $AwkCmd '{print $1,$4}'
 	rm -f ${DISTTMP}
 }
 
@@ -98,7 +98,7 @@ function writeTRNA {
 	TRNATMP="$$.trna.txt"
 
 	trnaAnnotations $1 > ${TRNATMP}
-	ntrna=`wc -l ${TRNATMP} | awk '{print $1}'`
+	ntrna=`wc -l ${TRNATMP} | $AwkCmd '{print $1}'`
 
 	if (( ntrna > 0 )); then 
 		trnacau=`findCAUtrna $1`
@@ -110,7 +110,7 @@ function writeTRNA {
 		
 			if (( distance <= 10 )); then
 				echo ">${aa}_${AC} gbac=${AC}; trna=${aa}; taxid=${TAXID}; distance=${distance}; ${DEFINITION}"
-				echo "$t" | awk -F ':' '{print $3}' 
+				echo "$t" | $AwkCmd -F ':' '{print $3}' 
 			fi
 		done
 	fi
diff --git a/scripts/bash_init.sh b/scripts/bash_init.sh
index 73b0185..bb60ba2 100644
--- a/scripts/bash_init.sh
+++ b/scripts/bash_init.sh
@@ -3,6 +3,8 @@
 # for setting up basic variables and functions
 #
 
+export AwkCmd="gawk"
+
 ########################
 #
 # General usage functions
@@ -25,8 +27,8 @@ function pushTmpDir {
 }
 
 function popTmpDir {
-	TMP_DIR=$(echo $TMP_DIR_STACK | awk '{print $1}')
-	TMP_DIR_STACK=$(echo $TMP_DIR_STACK | awk '{$1="";print $0}')
+	TMP_DIR=$(echo $TMP_DIR_STACK | $AwkCmd '{print $1}')
+	TMP_DIR_STACK=$(echo $TMP_DIR_STACK | $AwkCmd '{$1="";print $0}')
 	popd  >& /dev/null
 	rm -rf $TMP_DIR >& /dev/null
 	logdebug "Poping temp directory $TMP_DIR"
@@ -91,7 +93,7 @@ function fastaCount {
 function seqlength {
   cat $1 | \
   wc |\
-  awk -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
+  $AwkCmd -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
 }
 
 # extract a subseq from a fasta sequence
@@ -99,7 +101,7 @@ function seqlength {
 #   - $2 : First position of the subsequence (first position is numered 1), 
 #   - $3 : End of the subsequence (included in the subsequence)
 function cutseq {
-	awk -v from=$2 -v end=$3 'function printfasta(seq) {            \
+	$AwkCmd -v from=$2 -v end=$3 'function printfasta(seq) {            \
 									seqlen=length(seq);             \
 									for (i=1; i <= seqlen; i+=60)    \
 									   print substr(seq,i,60);      \
@@ -114,13 +116,13 @@ function cutseq {
 # a single sequence
 # 	- $1 : The fasta file containing the sequences to join
 function joinfasta {
-	awk '(NR==1 && /^>/) {print $0}                                 \
+	$AwkCmd '(NR==1 && /^>/) {print $0}                                 \
 	     ! /^>/          {print $0}' $1 |                           \
 		 formatfasta
 }
 
 function formatfasta {
-	awk  'function printfasta(seq) {                                \
+	$AwkCmd  'function printfasta(seq) {                                \
 									seqlen=length(seq);             \
 									for (i=1; i <= seqlen; i+=60)   \
 									   print substr(seq,i,60);      \