Index: head/biology/ddocent/Makefile
===================================================================
--- head/biology/ddocent/Makefile	(revision 500811)
+++ head/biology/ddocent/Makefile	(revision 500812)
@@ -1,68 +1,67 @@
 # $FreeBSD$
 
-PORTNAME=	dDocent
+PORTNAME=		dDocent
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.2.25
-PORTREVISION=	1
-CATEGORIES=	biology java
+DISTVERSION=		2.7.8
+CATEGORIES=		biology java perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Bash pipeline for RAD sequencing
 
 LICENSE=	MIT
 
 # ddocent test data do not unpack with FreeBSD 11.1 /usr/bin/unzip
 RUN_DEPENDS=	unzip>=0:archivers/unzip \
 		mawk>=0:lang/mawk \
 		gawk>=0:lang/gawk \
 		coreutils>=0:sysutils/coreutils \
 		gnuplot>=0:math/gnuplot \
 		parallel>=0:sysutils/parallel \
 		bash:shells/bash \
 		bwa>=0.7.13:biology/bwa \
 		cd-hit>=0:biology/cd-hit \
 		samtools>=1.3:biology/samtools \
 		vcftools>=0.1.15:biology/vcftools \
 		trimmomatic>=0:biology/trimmomatic \
 		bamtools>=0:biology/bamtools \
 		stacks>=0:biology/stacks \
 		rainbow>=0:biology/rainbow \
 		trimadap>=0:biology/trimadap \
 		seqtk>=0:biology/seqtk \
 		bedtools>=2.26.0:biology/bedtools \
 		pear-merger>=0:biology/pear-merger \
 		vcflib>=0:biology/vcflib \
-		freebayes:biology/freebayes
+		freebayes:biology/freebayes \
+		fastp:biology/fastp
 
 USES=		perl5 python shebangfix
-SHEBANG_FILES=	dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
 USE_JAVA=	yes
 USE_GITHUB=	yes
+
+SHEBANG_FILES=	dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
 GH_ACCOUNT=	jpuritz
 
 NO_BUILD=	yes
 NO_ARCH=	yes
 
-# These are on top of patch-dDocent, so don't apply them within the source
-# tree, or they'll get picked up by patch generators, and hard-code PREFIX.
-post-install:
-	${REINPLACE_CMD} -i '' \
-		-e 's|%%PREFIX%%|${PREFIX}|g' \
-		-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
-		-e 's|%%BASH%%|${LOCALBASE}/bin/bash|g' \
-		-e 's|python|${PYTHON_CMD}|g' \
-		${STAGEDIR}${PREFIX}/bin/dDocent
-
 do-install:
-	${MKDIR} ${STAGEDIR}${PREFIX}/bin
+	@${MKDIR} ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/dDocent \
 		${WRKSRC}/*.sh \
 		${FILESDIR}/ddocent-assembly-test \
 		${FILESDIR}/ddocent-assembly-test-cleanup \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${WRKSRC}/scripts/dDocent_filters \
 		${STAGEDIR}${PREFIX}/bin
+
+# These are on top of patch-dDocent, so don't apply them within the source
+# tree, or they'll get picked up by patch generators, and hard-code PREFIX.
+post-install:
+	@${REINPLACE_CMD} -i '' \
+		-e 's|SHELL=bash|SHELL=${LOCALBASE}/bin/bash|g' \
+		-e 's|python|${PYTHON_CMD}|g' \
+		${STAGEDIR}${PREFIX}/bin/dDocent
 
 .include <bsd.port.mk>
Index: head/biology/ddocent/distinfo
===================================================================
--- head/biology/ddocent/distinfo	(revision 500811)
+++ head/biology/ddocent/distinfo	(revision 500812)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1520345850
-SHA256 (jpuritz-dDocent-v2.2.25_GH0.tar.gz) = 903c3010b29b2ca95f7fe6099925948e4d3f21655668caff653df97dfa7ecf44
-SIZE (jpuritz-dDocent-v2.2.25_GH0.tar.gz) = 336804
+TIMESTAMP = 1556888100
+SHA256 (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 02aa297f602b55587782c959379cada8d8b0570973da75eb9f5786089a3ed485
+SIZE (jpuritz-dDocent-v2.7.8_GH0.tar.gz) = 345571
Index: head/biology/ddocent/files/ddocent-assembly-test
===================================================================
--- head/biology/ddocent/files/ddocent-assembly-test	(revision 500811)
+++ head/biology/ddocent/files/ddocent-assembly-test	(revision 500812)
@@ -1,380 +1,366 @@
 #!/usr/bin/env bash
 
 set -e
 
 ##########################################################################
 #   Function description:
 #       Pause until user presses return
 ##########################################################################
 
 pause()
 {
     local junk
     
     printf "Press return to continue..."
     read junk
 }
 
 
 ##########################################################################
 #   Not necessary if invoking scripts with "bash script-name" as shown
 #   in the dDocent tutorial, but supplied for completeness.  Tutorial
 #   scripts have also been patched upstream to usr /usr/bin/env, but
 #   we won't assume they'll all stay that way.
 ##########################################################################
 
 fix_bash_path()
 {
     # Don't echo these commands
     { set +x; } 2>/dev/null
     if [ $# != 1 ]; then
 	printf "Usage: $0 script\n"
 	exit 1
     fi
     sed -i.bak -e "s|#!/bin/bash|#!/usr/bin/env bash|g" $1
     set -x
 }
 
 
 ##########################################################################
 #   Main
 ##########################################################################
 
 ##########################################################################
 #   Workarounds for running dDocent from FreeBSD ports and Pkgsrc.
 #   Include this section in any scripts running dDocent commands.
 ##########################################################################
 
 # Hack to allow remake_reference.sh, etc. to find trimmomatic.
 # trimmomatic.jar and adapter files are not an executables and should not
 # be in PATH according to filesystem hierarchy standards, but the dDocent
 # scripts are coded to look for them there, because that's how dDocent
 # installs the bundled Trimmomatic.
 if [ -e /usr/local/share/java/classes/trimmomatic.jar ]; then
     export PATH=${PATH}:/usr/local/share/java/classes:/usr/local/share/trimmomatic/adapters
 elif [ -e $PKGSRC/lib/java/trimmomatic.jar ]; then
     export PATH=${PATH}:$PKGSRC/lib/java:$PKGSRC/share/trimmomatic/adapters
 else
     printf "Error: Trimmomatic is not installed in a known location.\n" >> /dev/stderr
 fi
 
 if ! pwd | fgrep dDocent-test; then
     mkdir -p dDocent-test
     cd dDocent-test
 fi
 
 # remake_reference.sh and some other scripts use GNU extensions in awk
 # commands.  Trick systems into using gawk to get around this without
 # having to patch every script.
 mkdir -p ddocent-bin
 ln -sf `which gawk` ddocent-bin/awk
 ln -sf `which python2.7` ddocent-bin/python
 export PATH=`pwd`/ddocent-bin:$PATH
 
 ##########################################################################
 #   Actual dDocent commands below
 ##########################################################################
 
 ##########################################################################
 #   Command sequence from the dDocent tutorial on Github.  See link below.
 ##########################################################################
 
 cat << EOM
 
 This script runs the test commands described at
 
 http://ddocent.com/assembly
 
 You may want to follow along on this web page as the script runs.  It will
 pause after each step to allow checking the output.
 
 EOM
 pause
 
 mkdir -p Data
 cd Data
 
 printf "Downloading and unpacking data.zip...\n"
 if [ -e data.zip ]; then
     mv data.zip /tmp/dDocent-data.zip
     rm -rf *
     mv /tmp/dDocent-data.zip data.zip
 else
     rm -rf *
     curl --insecure -L -o data.zip \
 	'https://www.dropbox.com/s/t09xjuudev4de72/data.zip?dl=0'
 fi
 
 # Hack: current data.zip contains data.zip.  ??!
 if [ ! -e simRRLs2.py ]; then
     yes | unzip data.zip || true
 fi
 ls -l
 pause
 
 set -x
 head SimRAD.barcodes
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cut -f2 SimRAD.barcodes > barcodes
 head barcodes
 { set +x; } 2>/dev/null
 pause
 
 set -x
 process_radtags -1 SimRAD_R1.fastq.gz -2 SimRAD_R2.fastq.gz -b barcodes \
     -e ecoRI --renz_2 mspI -r -i gzfastq
 ls | fgrep sample_ | head
 { set +x; } 2>/dev/null
 pause
 
 set -x
 rm *rem*
 { set +x; } 2>/dev/null
 pause
 
-rm -f Rename_for_dDocent.sh     # Always get the latest
-set -x
-curl --insecure -L -O https://github.com/jpuritz/dDocent/raw/master/Rename_for_dDocent.sh
-more Rename_for_dDocent.sh
 { set +x; } 2>/dev/null
 pause
 
 set -x
-bash Rename_for_dDocent.sh SimRAD.barcodes
+Rename_for_dDocent.sh SimRAD.barcodes
 { set +x; } 2>/dev/null
 
 set -x
 ls *.fq.gz
 { set +x; } 2>/dev/null
 pause
 
 set -x
 ls *.F.fq.gz > namelist
 sed -i'' -e 's/.F.fq.gz//g' namelist
 AWK1='BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}'
 AWK2='!/>/'
 AWK3='!/NNN/'
 PERLT='while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}'
 
 cat namelist | parallel --no-notice -j 8 "zcat {}.F.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.forward"
 cat namelist | parallel --no-notice -j 8 "zcat {}.R.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.reverse"
 cat namelist | parallel --no-notice -j 8 "paste -d '-' {}.forward {}.reverse | mawk '$AWK3' | sed 's/-/NNNNNNNNNN/' | perl -e '$PERLT' > {}.uniq.seqs"
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cat *.uniq.seqs > uniq.seqs
 for i in {2..20};
 do 
 echo $i >> pfile
 done
 cat pfile | parallel --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
 { set +x; } 2>/dev/null
 pause
 
 set -x
 more uniqseq.data
 { set +x; } 2>/dev/null
 pause
 
 set -x
 gnuplot << \EOF 
 set terminal dumb size 80, 30
 set autoscale
 set xrange [2:20] 
 unset label
 set title "Number of Unique Sequences with More than X Coverage (Counted within individuals)"
 set xlabel "Coverage"
 set ylabel "Number of Unique Sequences"
 plot 'uniqseq.data' with lines notitle
 pause -1
 EOF
 { set +x; } 2>/dev/null
 pause
 
 set -x
 parallel --no-notice -j 8 mawk -v x=4 \''$1 >= x'\' ::: *.uniq.seqs | cut -f2 | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$k\n";}' > uniqCperindv
 wc -l uniqCperindv
 { set +x; } 2>/dev/null
 pause
 
 set -x
 for ((i = 2; i <= 10; i++));
 do
 echo $i >> ufile
 done
 
 cat ufile | parallel --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
 { set +x; } 2>/dev/null
 pause
 
 set -x
 gnuplot << \EOF 
 set terminal dumb size 80, 30
 set autoscale 
 unset label
 set title "Number of Unique Sequences present in more than X Individuals"
 set xlabel "Number of Individuals"
 set ylabel "Number of Unique Sequences"
 plot 'uniqseq.peri.data' with lines notitle
 pause -1
 EOF
 { set +x; } 2>/dev/null
 pause
 
 set -x
 mawk -v x=4 '$1 >= x' uniqCperindv > uniq.k.4.c.4.seqs
 wc -l uniq.k.4.c.4.seqs
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cut -f2 uniq.k.4.c.4.seqs > totaluniqseq
 mawk '{c= c + 1; print ">Contig_" c "\n" $1}' totaluniqseq > uniq.fasta
 { set +x; } 2>/dev/null
 pause
 
 set -x
 sed -e 's/NNNNNNNNNN/\t/g' uniq.fasta | cut -f1 > uniq.F.fasta
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cd-hit-est -i uniq.F.fasta -o xxx -c 0.8 -T 0 -M 0 -g 1
 { set +x; } 2>/dev/null
 pause
 
 set -x
 mawk '{if ($1 ~ /Cl/) clus = clus + 1; else  print $3 "\t" clus}' xxx.clstr | sed 's/[>Contig_,...]//g' | sort -g -k1 > sort.contig.cluster.ids
 paste sort.contig.cluster.ids totaluniqseq > contig.cluster.totaluniqseq
 sort -k2,2 -g contig.cluster.totaluniqseq | sed -e 's/NNNNNNNNNN/\t/g' > rcluster
 { set +x; } 2>/dev/null
 pause
 
 set -x
 head rcluster
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cut -f2 rcluster | uniq | wc -l
 { set +x; } 2>/dev/null
 pause
 
 set -x
 rainbow div -i rcluster -o rbdiv.out
 { set +x; } 2>/dev/null
 pause
 
 set -x
 rainbow div -i rcluster -o rbdiv.out -f 0.5 -K 10
 { set +x; } 2>/dev/null
 pause
 
 set -x
 rainbow merge -o rbasm.out -a -i rbdiv.out
 { set +x; } 2>/dev/null
 pause
 
 set -x
 rainbow merge -o rbasm.out -a -i rbdiv.out -r 2
 { set +x; } 2>/dev/null
 pause
 
 # If missing fdesc mount for bash, <(echo "E") will not work
 # cat rbasm.out <(echo "E") |sed 's/[0-9]*:[0-9]*://g' | mawk ' {
 set -x
 echo "E" > endfile
 cat rbasm.out endfile |sed 's/[0-9]*:[0-9]*://g' | mawk ' {
 if (NR == 1) e=$2;
 else if ($1 ~/E/ && lenp > len1) {c=c+1; print ">dDocent_Contig_" e "\n" seq2 "NNNNNNNNNN" seq1; seq1=0; seq2=0;lenp=0;e=$2;fclus=0;len1=0;freqp=0;lenf=0}
 else if ($1 ~/E/ && lenp <= len1) {c=c+1; print ">dDocent_Contig_" e "\n" seq1; seq1=0; seq2=0;lenp=0;e=$2;fclus=0;len1=0;freqp=0;lenf=0}
 else if ($1 ~/C/) clus=$2;
 else if ($1 ~/L/) len=$2;
 else if ($1 ~/S/) seq=$2;
 else if ($1 ~/N/) freq=$2;
 else if ($1 ~/R/ && $0 ~/0/ && $0 !~/1/ && len > lenf) {seq1 = seq; fclus=clus;lenf=len}
 else if ($1 ~/R/ && $0 ~/0/ && $0 ~/1/) {seq1 = seq; fclus=clus; len1=len}
 else if ($1 ~/R/ && $0 ~!/0/ && freq > freqp && len >= lenp || $1 ~/R/ && $0 ~!/0/ && freq == freqp && len > lenp) {seq2 = seq; lenp = len; freqp=freq}
 }' > rainbow.fasta
 { set +x; } 2>/dev/null
 pause
 
 set -x
 cd-hit-est -i rainbow.fasta -o referenceRC.fasta -M 0 -T 0 -c 0.9
 { set +x; } 2>/dev/null
 pause
 
-rm -f remake_reference.sh
-set -x
-curl --insecure -L -O https://github.com/jpuritz/dDocent/raw/master/scripts/remake_reference.sh
-more remake_reference.sh
-#fix_bash_path remake_reference.sh
-
-bash remake_reference.sh 4 4 0.90 PE 2
+remake_reference.sh 4 4 0.90 PE 2
 { set +x; } 2>/dev/null
 pause
 
-rm -f ReferenceOpt.sh
-set -x
-curl --insecure -L -O https://github.com/jpuritz/dDocent/raw/master/scripts/ReferenceOpt.sh
-more ReferenceOpt.sh
+ReferenceOpt.sh
 
 bash ReferenceOpt.sh 4 8 4 8 PE 16
 { set +x; } 2>/dev/null
 pause
 
 set -x
 bash remake_reference.sh 4 4 0.90 PE 2
 head reference.fasta
 { set +x; } 2>/dev/null
 pause
 
 set -x
 wc -l reference.fasta
 { set +x; } 2>/dev/null
 pause
 
 set -x
 mawk '/>/' reference.fasta | wc -l
 { set +x; } 2>/dev/null
 pause
 
 set -x
 mawk '/^NAATT.*N*.*CCGN$/' reference.fasta | wc -l
 grep '^NAATT.*N*.*CCGN$' reference.fasta | wc -l
 { set +x; } 2>/dev/null
 pause
 
 printf "Bonus Section: Optimize reference assemblies? (takes a long time) y/[n] "
 read bonus
 if [ 0$bonus = 0y ]; then
     set -x
-    curl -L -O https://raw.githubusercontent.com/jpuritz/dDocent/master/scripts/RefMapOpt.sh
     { set +x; } 2>/dev/null
     printf "Running dDocent to trim reads.\n"
     pause
     set -x
     cat << EOM | dDocent || true
 yes
 8
 10g
 yes
 no
 no
 no
 bacon@uwm.edu
 EOM
-    bash RefMapOpt.sh 4 8 4 8 0.9 64 PE
+    RefMapOpt.sh 4 8 4 8 0.9 64 PE
     { set +x; } 2>/dev/null
     pause
     more mapping.results
     pause
 fi
Index: head/biology/ddocent/files/patch-dDocent
===================================================================
--- head/biology/ddocent/files/patch-dDocent	(revision 500811)
+++ head/biology/ddocent/files/patch-dDocent	(revision 500812)
@@ -1,134 +1,73 @@
---- dDocent.orig	2018-04-20 00:10:34 UTC
+--- dDocent.orig	2019-05-03 12:59:20 UTC
 +++ dDocent
-@@ -1,6 +1,9 @@
+@@ -1,5 +1,6 @@
  #!/usr/local/bin/bash
  export LC_ALL=en_US.UTF-8
- 
 +# GNU Parallel uses $SHELL and has issues with [t]csh
-+export SHELL=%%BASH%%
-+
- ##########dDocent##########
- VERSION='2.2.25'
- #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.
-@@ -27,15 +30,15 @@ do
- 	fi
- done
+ export SHELL=bash
  
--if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null| grep -q 'trim' ; then
--	TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
-+if [ -e %%JAVAJARDIR%%/trimmomatic.jar ]; then
-+       TRIMMOMATIC=%%JAVAJARDIR%%/trimmomatic.jar
- 	else
-     echo "The dependency trimmomatic is not installed or is not in your" '$PATH'"."
-     NUMDEP=$((NUMDEP + 1))
- 	fi
- 
--if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | grep -q 'Tru' ; then
--	ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
-+if [ -e %%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa ]; then
-+       ADAPTERS=%%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa
- 	else
-     echo "The file listing adapters (included with trimmomatic) is not installed or is not in your" '$PATH'"."
-     NUMDEP=$((NUMDEP + 1))
-@@ -80,6 +83,7 @@ FREEB=(`freebayes | grep -oh 'v[0-9].*' 
-         	exit 1
-         fi         	
- VCFTV=$(vcftools | grep VCF | grep -oh '[0-9]*[a-z]*)$' | sed 's/[a-z)]//')
-+	echo $VCFTV
- 	if [ "$VCFTV" -lt "10" ]; then
-         	echo "The version of VCFtools installed in your" '$PATH' "is not optimized for dDocent."
-         	echo "Please install at least version 0.1.11"
-@@ -89,7 +93,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '
+ ##########dDocent##########
+@@ -83,7 +84,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '[0-9]*[a-z]*)$
          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" '$PATH' "is not optimized for dDocent."
          	echo "Please install at least version 0.7.13"
-@@ -107,13 +111,12 @@ BTC=$( bedtools --version | mawk '{print
- 		exit 1	
- 	fi
- 		
--if ! awk --version | fgrep -v GNU &>/dev/null; then
-+if ! awk --version | fgrep GNU &>/dev/null; then
-          awk=gawk
-     else
-          awk=awk
- fi
+@@ -481,7 +482,7 @@ if [ "$SNP" != "no" ]; then
+         		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}
+         	}'
+-                ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos2 --memfree $MAXMemory -j 4 --no-notice "call_genos2 {} 2> /dev/null"
++                ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --bar --halt now,fail=1 --env call_genos2 --memfree $MAXMemory -j 4 --no-notice "call_genos2 {} 2> /dev/null"
+                 if [ -f "freebayes.error" ]; then
+                         echo -e "\n\n\nFreeBayes has failed when trying to finish a previously failed instance.  Memory and processor settings need to be drastically reconfigured"
+                         ERROR3=1
+@@ -505,7 +506,7 @@ if [ "$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=5 --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=5 --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice "call_genos {} 2> /dev/null"
  
--
- if [ $NUMDEP -gt 0 ]; then
- 	echo -e "\nPlease install all required software before running dDocent again."
- 	exit 1
-@@ -291,9 +294,9 @@ echo "Using BWA to map reads."
-         	for i in "${NAMES[@]}"
-         	do
-         	if [ -f "$i.R2.fq.gz" ]; then
--        		bwa mem reference.fasta $i.R1.fq.gz $i.R2.fq.gz -L 20,5 -I $INSERT,$SD,$INSERTH,$INSERTL -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" 2> bwa.$i.log | mawk '$6 !~/[2-9].[SH]/ && $6 !~ /[1-9][0-9].[SH]/' | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2>$i.bam.log
-+        		bwa mem -L 20,5 -I $INSERT,$SD,$INSERTH,$INSERTL -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" reference.fasta $i.R1.fq.gz $i.R2.fq.gz 2> bwa.$i.log | mawk '$6 !~/[2-9].[SH]/ && $6 !~ /[1-9][0-9].[SH]/' | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2>$i.bam.log
-         	else
--        		bwa mem reference.fasta $i.R1.fq.gz -L 20,5 -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" 2> bwa.$i.log | mawk '$6 !~/[2-9].[SH]/ && $6 !~ /[1-9][0-9].[SH]/' | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2>$i.bam.log
-+        		bwa mem -L 20,5 -t $NUMProc -a -M -T 10 -A $optA -B $optB -O $optO -R "@RG\tID:$i\tSM:$i\tPL:Illumina" reference.fasta $i.R1.fq.gz 2> bwa.$i.log | mawk '$6 !~/[2-9].[SH]/ && $6 !~ /[1-9][0-9].[SH]/' | samtools view -@$NUMProc -q 1 -SbT reference.fasta - > $i.bam 2>$i.bam.log
-         	fi
-         	samtools sort -@$NUMProc $i.bam -o $i.bam 
- 		mv $i.bam $i-RG.bam
-@@ -388,10 +391,10 @@ if [ "$SNP" != "no" ]; then
- 	}
- 	export -f call_genos
  
--	ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice call_genos {}
-+	ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --env call_genos --memfree $MAXMemory -j $NUMProc --no-notice call_genos {}
- ####	
--	#ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --memfree $MAXMemory -j $FB1 --no-notice --delay 1 freebayes -L bamlist.list -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10
--	#ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --memfree $MAXMemory -j $FB1 --no-notice "samtools view -b -L mapped.{}.bed | freebayes -c -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10"
-+	#ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --memfree $MAXMemory -j $FB1 --no-notice --delay 1 freebayes -L bamlist.list -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10
-+	#ls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | gshuf | parallel --memfree $MAXMemory -j $FB1 --no-notice "samtools view -b -L mapped.{}.bed | freebayes -c -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10"
+ 	if [ -f "freebayes.error" ]; then
+@@ -541,7 +542,7 @@ if [ "$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=5 --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=5 --env call_genos --memfree $MAXMemory -j $NumP --no-notice "call_genos {} 2> /dev/null" 
+         fi
+     fi
  
+@@ -575,7 +576,7 @@ 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
+ 	fi
  
- 	rm mapped.*.bed 
-@@ -447,8 +450,8 @@ fi
+@@ -1132,6 +1133,8 @@ 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 &> $1.trim.log
-@@ -747,7 +750,14 @@ else
+ if [[ "$OSTYPE" == "darwin"* ]]; then
+ 	NUMProc=( `sysctl hw.ncpu | cut -f2 -d " " `)
++elif [[ "$OSTYPE" == "FreeBSD" ]]; then
++	NUMProc=( `sysctl -n hw.ncpu` )
+ else
+ 	NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` ) 
  fi
- 
- #Tries to get number of processors, if not asks user
--NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` ) 
-+if [ `uname` = Linux ]; then
-+    NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` ) 
-+elif [ `uname` = FreeBSD ]; then
-+    NUMProc=( `sysctl -n hw.ncpu` ) 
-+else
-+    printf "Unsupported platform: `uname`\n"
-+    exit 1
-+fi
- NUMProc=$(($NUMProc + 0)) 
- 
- echo "dDocent detects $NUMProc processors available on this system."
-@@ -764,7 +774,15 @@ if [ $NUMProc -lt 1 ]; then
- fi
- 
+@@ -1154,6 +1157,9 @@ fi
  #Tries to get maximum system memory, if not asks user
--MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))G
-+if [ `uname` = Linux ]; then
-+    MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))G
-+elif [ `uname` = FreeBSD ]; then
-+    MAXMemory=`sysctl -n hw.realmem`
-+    MAXMemory=$((MAXMemory / 1073741824))G
-+else
-+    printf "Unsupported platform: `uname`\n"
-+    exit 1
-+fi
+ if [[ "$OSTYPE" == "darwin"* ]]; then
+ 	MAXMemory=0
++elif [[ "$OSTYPE" == "FreeBSD" ]]; then
++	MAXMemory=`sysctl -n hw.realmem`
++	MAXMemory=$((MAXMemory / 1073741824))G
+ else
+ 	MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))
  
- echo "dDocent detects $MAXMemory maximum memory available on this system."
- echo "Please enter the maximum memory to use for this analysis. The size can be postfixed with 
Index: head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh
===================================================================
--- head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh	(nonexistent)
+++ head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh	(revision 500812)
@@ -0,0 +1,11 @@
+--- scripts/ReferenceOpt.sh.orig	2019-05-03 12:58:47 UTC
++++ scripts/ReferenceOpt.sh
+@@ -400,7 +400,7 @@ done
+ 
+ cut -f4 -d " " kopt.data > plot.kopt.data
+ gnuplot << \EOF
+-set terminal dumb size 120, 30
++set terminal dumb size 80, 30
+ set autoscale
+ unset label
+ set title "Histogram of number of reference contigs"

Property changes on: head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/ddocent/pkg-plist
===================================================================
--- head/biology/ddocent/pkg-plist	(revision 500811)
+++ head/biology/ddocent/pkg-plist	(revision 500812)
@@ -1,17 +1,16 @@
 bin/ErrorCount.sh
 bin/RefMapOpt.sh
-bin/ReferenceOpt.hyb.sh
 bin/ReferenceOpt.sh
 bin/Rename_SequenceFiles.sh
 bin/Rename_for_dDocent.sh
 bin/Rename_for_dDocent_with-INDEX.sh
 bin/dDocent
 bin/dDocent_filters
 bin/dDocent_ngs.sh
 bin/ddocent-assembly-test
 bin/ddocent-assembly-test-cleanup
 bin/filter_hwe_by_pop.pl
 bin/filter_missing_ind.sh
 bin/pop_missing_filter.sh
 bin/remake_reference.sh
 bin/remove.bad.hap.loci.sh