$NetBSD$

Fixes for GNU sort, awk, shuf naming. Ensure $SHELL is bash. Path cleanup.
--- dDocent.orig	2018-06-15 14:58:07 UTC
+++ dDocent
@@ -1,6 +1,10 @@
 #!/usr/bin/env bash
+
 export LC_ALL=en_US.UTF-8
 
+# GNU Parallel uses $SHELL and has issues with [t]csh
+export SHELL=%%PREFIX%%/bin/bash
+
 ##########dDocent##########
 VERSION='2.5.2'
 #This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD (SE or PE), ezRAD (SE or PE) data, or SE RAD data.
@@ -27,19 +31,19 @@ do
 	fi
 done
 
-if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null| grep -q 'trim' ; then
-	TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
-	else
+if [ -e %%JAVAJARDIR%%/trimmomatic.jar ]; then
+	TRIMMOMATIC=%%JAVAJARDIR%%/trimmomatic.jar
+else
     echo "The dependency trimmomatic is not installed or is not in your" '$PATH'"."
     NUMDEP=$((NUMDEP + 1))
-	fi
+fi
 
-if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | grep -q 'Tru' ; then
-	ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
-	else
+if [ -e %%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa ]; then
+	ADAPTERS=%%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa
+else
     echo "The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
     NUMDEP=$((NUMDEP + 1))
-    fi
+fi
 
 SAMV1=$(samtools 2>&1 >/dev/null | grep Ver | sed -e 's/Version://' | cut -f2 -d " " | sed -e 's/-.*//' | cut -c1)
 SAMV2=$(samtools 2>&1 >/dev/null | grep Ver | sed -e 's/Version://' | cut -f2 -d " " | sed -e 's/-.*//' | cut -c3)
@@ -96,7 +100,8 @@ VCFTV=$(vcftools | grep VCF | grep -oh '
         elif [ "$VCFTV" -ge "12" ]; then
                 VCFGTFLAG="--max-missing"
 	fi
-BWAV=$(bwa 2>&1 | mawk '/Versi/' | sed 's/Version: //g' | sed 's/0.7.//g' | sed 's/-.*//g' | cut -c 1-2)
+BWAV=$(bwa 2>&1 | mawk '/Versi/' | sed 's/Version: //g' | sed 's/0.7.//g' | sed
+ 's/a*-.*//g')
 	if [ "$BWAV" -lt "13" ]; then
         	echo "The version of bwa installed in your" '$PATH' "is not optimized for dDocent."
         	echo "Please install at least version 0.7.13"
@@ -114,10 +119,16 @@ BTC=$( bedtools --version | mawk '{print
 		exit 1	
 	fi
 		
-if ! awk --version | fgrep -v GNU &>/dev/null; then
-         awk=gawk
-    else
-         awk=awk
+if ! awk --version | fgrep -q GNU; then
+	awk=gawk
+else
+	awk=awk
+fi
+
+if ! sort --version | fgrep -q GNU; then
+	sort=gsort
+else
+	sort=sort
 fi
 
 if [ $NUMDEP -gt 0 ]; then
@@ -391,18 +402,18 @@ if [ "$SNP" != "no" ]; then
 			mawk -v OFS='\t' {'print $1,$2'} reference.fasta.fai > genome.file
 			cat namelist | parallel -j $FB2 "bedtools coverage -b {}-RG.bam -a mapped.bed -counts -sorted -g genome.file > {}.cov.stats"
 		fi
-		cat *.cov.stats | sort -k1,1 -k2,2n | bedtools merge -i - -c 4 -o sum > cov.stats
+		cat *.cov.stats | $sort -k1,1 -k2,2n | bedtools merge -i - -c 4 -o sum > cov.stats
 	fi
 		
 	if head -1 reference.fasta | grep -e 'dDocent' reference.fasta 1>/dev/null; then
 	
-		DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
+		DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
 		CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$NUMProc'"}')
 	else
-		DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
+		DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
 		CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$NUMProc'"}')
 	fi
-	mawk -v x=$DP '$4 < x' cov.stats |sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1} 
+	mawk -v x=$DP '$4 < x' cov.stats |$sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1} 
 	{
 	len=$3-$2;lc=len*$4;cov = cov + lc
 	if ( cov < cutoff) {x="mapped."i".bed";print $1"\t"$2"\t"$3 > x}
@@ -440,7 +451,7 @@ if [ "$SNP" != "no" ]; then
 	
 	rm freebayes.error freebayes.log &> /dev/null
 	
-	ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice "call_genos {} 2> /dev/null"
+	ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice "call_genos {} 2> /dev/null"
 
 
 	if [ -f "freebayes.error" ]; then
@@ -450,13 +461,13 @@ if [ "$SNP" != "no" ]; then
 		LIM=$(( $NUMProc * 2 ))
         	if head -1 reference.fasta | grep -e 'dDocent' reference.fasta 1>/dev/null; then
 
-                	DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
+                	DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
                 	CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$LIM'"}')
         	else
-                	DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
+                	DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
                 	CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$LIM'"}')
         	fi
-        	mawk -v x=$DP '$4 < x' cov.stats |sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1}
+        	mawk -v x=$DP '$4 < x' cov.stats |$sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1}
         	{ len=$3-$2;lc=len*$4;cov = cov + lc
         	if ( cov < cutoff) {x="mapped."i".bed";print $1"\t"$2"\t"$3 > x}
         	else {i=i+1; x="mapped."i".bed"; print $1"\t"$2"\t"$3 > x; cov=0}
@@ -467,7 +478,7 @@ if [ "$SNP" != "no" ]; then
 		echo "Using FreeBayes to call SNPs again"
 		NumP=$(( $NUMProc / 4 ))
 		NumP=$(( $NumP * 3 ))
-		ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null" 
+		ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null" 
         fi
 
 	if [ -f "freebayes.error" ]; then
@@ -477,13 +488,13 @@ if [ "$SNP" != "no" ]; then
 		LIM=$(( $NUMProc * 4 ))
         	if head -1 reference.fasta | grep -e 'dDocent' reference.fasta 1>/dev/null; then
 
-                	DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
+                	DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.001;@l=<>;print $l[int($d*@l)]')
                 	CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$LIM'"}')
         	else
-                	DP=$(mawk '{print $4}' cov.stats | sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
+                	DP=$(mawk '{print $4}' cov.stats | $sort -rn | perl -e '$d=.00005;@l=<>;print $l[int($d*@l)]')
                 	CC=$( mawk -v x=$DP '$4 < x' cov.stats | mawk '{len=$3-$2;lc=len*$4;tl=tl+lc} END {OFMT = "%.0f";print tl/"'$LIM'"}')
         	fi
-        	mawk -v x=$DP '$4 < x' cov.stats |sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1}
+        	mawk -v x=$DP '$4 < x' cov.stats |$sort -V -k1,1 -k2,2 | mawk -v cutoff=$CC 'BEGIN{i=1}
         	{ len=$3-$2;lc=len*$4;cov = cov + lc
         	if ( cov < cutoff) {x="mapped."i".bed";print $1"\t"$2"\t"$3 > x}
         	else {i=i+1; x="mapped."i".bed"; print $1"\t"$2"\t"$3 > x; cov=0}
@@ -492,7 +503,7 @@ if [ "$SNP" != "no" ]; then
             	NumP=$(( $NumP / 4 ))
                 NumP=$(( $NumP * 3 ))
 		echo "Using FreeBayes to call SNPs again"
-                ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
+                ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null"
 	fi
 
 	if [ -f "freebayes.error" ]; then
@@ -560,8 +571,8 @@ fi
 
 #Function for trimming reads using trimmomatic
 trim_reads(){
-	TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
-    	ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
+	TRIMMOMATIC=%%JAVAJARDIR%%/trimmomatic.jar
+	ADAPTERS=%%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa
 
 	if [ -f $1.R.fq.gz ]; then	
 		java -Xmx2g -jar $TRIMMOMATIC PE -threads 2 -phred33 $1.F.fq.gz $1.R.fq.gz $1.R1.fq.gz $1.unpairedF.fq.gz $1.R2.fq.gz $1.unpairedR.fq.gz ILLUMINACLIP:$ADAPTERS:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:10 $TW &> $1.trim.log
@@ -617,7 +628,7 @@ if [ -z "$CUTOFF" ]; then
 	do 
 	echo $i >> pfile
 	done
-	cat pfile | parallel -j $NUMProc --no-notice "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniq.seqs | wc -l" | mawk  '{gsub("xxx","\t",$0); print;}'| sort -g > uniqseq.data
+	cat pfile | parallel -j $NUMProc --no-notice "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniq.seqs | wc -l" | mawk  '{gsub("xxx","\t",$0); print;}'| $sort -g > uniqseq.data
 	rm pfile
 
 
@@ -652,7 +663,7 @@ export -f special_uniq
 
 
 if [[ "$ATYPE" == "RPE" || "$ATYPE" == "ROL" ]]; then
-  	parallel --no-notice -j $NUMProc --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | sort --parallel=$NUMProc -S 2G | uniq -c > uniqCperindv
+  	parallel --no-notice -j $NUMProc --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | $sort --parallel=$NUMProc -S 2G | uniq -c > uniqCperindv
 else
 	parallel --no-notice -j $NUMProc mawk -v x=$CUTOFF \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}' > uniqCperindv
 fi
@@ -670,7 +681,7 @@ if [ -z "$CUTOFF2" ]; then
 	echo $i >> ufile
 	done
 
-	cat ufile | parallel -j $NUMProc --no-notice "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniqCperindv | wc -l" | mawk  '{gsub("xxx","\t",$0); print;}'| sort -g > uniqseq.peri.data
+	cat ufile | parallel -j $NUMProc --no-notice "echo -n {}xxx && mawk -v x={} '\$1 >= x' uniqCperindv | wc -l" | mawk  '{gsub("xxx","\t",$0); print;}'| $sort -g > uniqseq.peri.data
 	rm ufile
 
 	
@@ -734,7 +745,7 @@ if [ ${NAMES[@]:(-1)}.F.fq.gz -nt ${NAME
 		cat namelist | parallel --no-notice -j $NUMProc "zcat {}.F.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.forward"
 		cat namelist | parallel --no-notice -j $NUMProc "zcat {}.R.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.reverse"
 		if [ "$ATYPE" = "RPE" ]; then
-			cat namelist | parallel --no-notice -j $NUMProc "paste {}.forward {}.reverse | sort -k1 -S 200M > {}.fr"
+			cat namelist | parallel --no-notice -j $NUMProc "paste {}.forward {}.reverse | $sort -k1 -S 200M > {}.fr"
 			cat namelist | parallel --no-notice -j $NUMProc "cut -f1 {}.fr | uniq -c > {}.f.uniq && cut -f2 {}.fr > {}.r"
 			cat namelist | parallel --no-notice -j $NUMProc "mawk '$AWK4' {}.f.uniq > {}.f.uniq.e" 
 			cat namelist | parallel --no-notice -j $NUMProc "paste -d '-' {}.f.uniq.e {}.r | mawk '$AWK3'| sed 's/-/NNNNNNNNNN/' | sed -e '$SED1' | sed -e '$SED2'> {}.uniq.seqs"
@@ -805,7 +816,7 @@ getAssemblyInfo
 fi
 
 if [[ "$ATYPE" == "RPE" || "$ATYPE" == "ROL" ]]; then
-  	parallel --no-notice -j $NUMProc --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | sort --parallel=$NUMProc -S 2G | uniq -c > uniqCperindv
+  	parallel --no-notice -j $NUMProc --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | $sort --parallel=$NUMProc -S 2G | uniq -c > uniqCperindv
 else
 	parallel --no-notice -j $NUMProc mawk -v x=$CUTOFF \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}' > uniqCperindv
 fi
@@ -817,16 +828,16 @@ if [[ "$ATYPE" == "RPE" || "$ATYPE" == "
   parallel --no-notice -j $NUMProc mawk -v x=$CUTOFF \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | sed 's/NNNNNNNNNN/-/' >  total.uniqs
   cut -f 1 -d "-" total.uniqs > total.u.F
   cut -f 2 -d "-" total.uniqs > total.u.R
-  paste total.u.F total.u.R | sort -k1 --parallel=$NUMProc -S 2G > total.fr
+  paste total.u.F total.u.R | $sort -k1 --parallel=$NUMProc -S 2G > total.fr
  
-  parallel --no-notice --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | sort --parallel=$NUMProc -S 2G | uniq -c > total.f.uniq
+  parallel --no-notice --env special_uniq special_uniq $CUTOFF {} ::: *.uniq.seqs  | $sort --parallel=$NUMProc -S 2G | uniq -c > total.f.uniq
   join -1 2 -2 1 -o 1.1,1.2,2.2 total.f.uniq total.fr | mawk '{print $1 "\t" $2 "NNNNNNNNNN" $3}' | mawk -v x=$CUTOFF2 '$1 >= x' > uniq.k.$CUTOFF.c.$CUTOFF2.seqs
   rm total.uniqs total.u.* total.fr total.f.uniq* 
   
 else
 	parallel --no-notice mawk -v x=$CUTOFF \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}' | mawk -v x=$CUTOFF2 '$1 >= x' > uniq.k.$CUTOFF.c.$CUTOFF2.seqs
 fi
-sort -k1 -r -n uniq.k.$CUTOFF.c.$CUTOFF2.seqs | cut -f 2 > totaluniqseq
+$sort -k1 -r -n uniq.k.$CUTOFF.c.$CUTOFF2.seqs | cut -f 2 > totaluniqseq
 mawk '{c= c + 1; print ">dDocent_Contig_" c "\n" $1}' totaluniqseq > uniq.full.fasta
 LENGTH=$(mawk '!/>/' uniq.full.fasta  | mawk '(NR==1||length<shortest){shortest=length} END {print shortest}')
 LENGTH=$(($LENGTH * 3 / 4))
@@ -861,21 +872,21 @@ if [[ "$ATYPE" == "PE" || "$ATYPE" == "R
 		sed -e 's/NNNNNNNNNN/	/g' uniq.fasta | cut -f1 > uniq.F.fasta
 	  	CDHIT=$(python -c "print (max("$simC" - 0.1,0.8))")
 	  	cd-hit-est -i uniq.F.fasta -o xxx -c $CDHIT -T $NUMProc -M 0 -g 1 -d 100 &>cdhit.log
-	  	mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids
+	  	mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | $sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids
 	  	paste sort.contig.cluster.ids totaluniqseq > contig.cluster.totaluniqseq
           
      	else
-        	sed -e 's/NNNNNNNNNN/	/g' totaluniqseq | cut -f1 | sort --parallel=$NUMProc -S 2G| uniq | mawk '{c= c + 1; print ">dDocent_Contig_" c "\n" $1}' > uniq.F.fasta
+        	sed -e 's/NNNNNNNNNN/	/g' totaluniqseq | cut -f1 | $sort --parallel=$NUMProc -S 2G| uniq | mawk '{c= c + 1; print ">dDocent_Contig_" c "\n" $1}' > uniq.F.fasta
 		CDHIT=$(python -c "print (max("$simC" - 0.1,0.8))")
 		cd-hit-est -i uniq.F.fasta -o xxx -c $CDHIT -T $NUMProc -M 0 -g 1 -d 100 &>cdhit.log
-  		mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids
+  		mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | $sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids
   		paste sort.contig.cluster.ids <(mawk '!/>/' uniq.F.fasta) > contig.cluster.Funiq
-  		sed -e 's/NNNNNNNNNN/	/g' totaluniqseq | sort --parallel=$NUMProc -k1 -S 2G | mawk '{print $0 "\t" NR}'  > totaluniqseq.CN
+  		sed -e 's/NNNNNNNNNN/	/g' totaluniqseq | $sort --parallel=$NUMProc -k1 -S 2G | mawk '{print $0 "\t" NR}'  > totaluniqseq.CN
   		join -t $'\t' -1 3 -2 1 contig.cluster.Funiq totaluniqseq.CN -o 2.3,1.2,2.1,2.2 > contig.cluster.totaluniqseq
 	fi	
 	
 	#CD-hit output is converted to rainbow format
-	sort -k2,2 -g contig.cluster.totaluniqseq -S 2G --parallel=$NUMProc | sed -e 's/NNNNNNNNNN/	/g' > rcluster
+	$sort -k2,2 -g contig.cluster.totaluniqseq -S 2G --parallel=$NUMProc | sed -e 's/NNNNNNNNNN/	/g' > rcluster
 	rainbow div -i rcluster -o rbdiv.out -f 0.5 -K 10
         CLUST=(`tail -1 rbdiv.out | cut -f5`)
 	CLUST1=$(( $CLUST / 100 + 1))
@@ -944,9 +955,9 @@ if [[ "$ATYPE" == "HYB" ]];then
 		sed -e 's/NNNNNNNNNN/	/g' uniq.ua.fasta | cut -f1 > uniq.F.ua.fasta
 		CDHIT=$(python -c "print(max("$simC" - 0.1,0.8))")
 		cd-hit-est -i uniq.F.ua.fasta -o xxx -c $CDHIT -T 0 -M 0 -g 1 -d 100 &>cdhit.log
-		mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids.ua
+		mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>dDocent_Contig_,...]//g' | $sort -g -k1 -S 2G --parallel=$NUMProc > sort.contig.cluster.ids.ua
 		paste sort.contig.cluster.ids.ua totaluniqseq.ua > contig.cluster.totaluniqseq.ua
-		sort -k2,2 -g -S 2G --parallel=$NUMProc contig.cluster.totaluniqseq.ua | sed -e 's/NNNNNNNNNN/	/g' > rcluster.ua
+		$sort -k2,2 -g -S 2G --parallel=$NUMProc contig.cluster.totaluniqseq.ua | sed -e 's/NNNNNNNNNN/	/g' > rcluster.ua
 		#CD-hit output is converted to rainbow format
 		rainbow div -i rcluster.ua -o rbdiv.ua.out -f 0.5 -K 10
 		if [ "$ATYPE" == "PE" ]; then
@@ -1028,7 +1039,14 @@ else
 fi
 
 #Tries to get number of processors, if not asks user
-NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` ) 
+if [ `uname` = Linux ]; then
+    NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` )
+elif [ `uname` = FreeBSD ]; then
+    NUMProc=( `sysctl -n hw.ncpu` )
+else
+    printf "Unsupported platform: `uname`\n"
+    exit 1
+fi
 NUMProc=$(($NUMProc + 0)) 
 
 echo "dDocent detects $NUMProc processors available on this system."
@@ -1045,7 +1063,16 @@ if [ $NUMProc -lt 1 ]; then
 fi
 
 #Tries to get maximum system memory, if not asks user
-MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))
+if [ `uname` = Linux ]; then
+    MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d "
+") / 1048576))G
+elif [ `uname` = FreeBSD ]; then
+    MAXMemory=`sysctl -n hw.realmem`
+    MAXMemory=$((MAXMemory / 1073741824))G
+else
+    printf "Unsupported platform: `uname`\n"
+    exit 1
+fi
 
 echo "dDocent detects $MAXMemory gigabytes of maximum memory available on this system."
 echo "Please enter the maximum memory to use for this analysis in gigabytes"