ddocent: bump to 2.5.2 (wip)

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: ddocent: bump to 2.5.2 (wip)
From: Winston Weinert <winston%ml1.net@localhost>
Date: Thu, 14 Jun 2018 07:50:22 +0000
Module Name:	pkgsrc-wip
Committed By:	Winston Weinert <winston%ml1.net@localhost>
Pushed By:	winston
Date:		Thu Jun 14 02:50:22 2018 -0500
Changeset:	2aa7a6ff3f466162d07f6c30bb8202026fcd2270

Modified Files:
	ddocent/Makefile
	ddocent/PLIST
	ddocent/distinfo
	ddocent/patches/patch-dDocent
Added Files:
	ddocent/TODO

Log Message:
ddocent: bump to 2.5.2 (wip)

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2aa7a6ff3f466162d07f6c30bb8202026fcd2270

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ddocent/Makefile              |  2 +-
 ddocent/PLIST                 |  1 -
 ddocent/TODO                  |  2 ++
 ddocent/distinfo              | 10 +++---
 ddocent/patches/patch-dDocent | 77 +++++++++++++++++++++++++------------------
 5 files changed, 53 insertions(+), 39 deletions(-)

diffs:
diff --git a/ddocent/Makefile b/ddocent/Makefile
index 3eb5d71482..4363cd996a 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -57,7 +57,7 @@ USE_TOOLS=	bash perl unzip
 
 ERROR: [check-interpreter.mk] The interpreter "/usr/bin/env" of "/usr/pkgsrc/wip/ddocent/work/.destdir/usr/pkg/bin/ddocent-test" is not allowed.
 
-PORTVERSION=	2.2.25
+PORTVERSION=	2.5.2
 JAVAJARDIR=	${PREFIX}/lib/java
 
 INSTALLATION_DIRS=	bin
diff --git a/ddocent/PLIST b/ddocent/PLIST
index fa7987a570..9de3aea86c 100644
--- a/ddocent/PLIST
+++ b/ddocent/PLIST
@@ -1,7 +1,6 @@
 @comment $NetBSD$
 bin/ErrorCount.sh
 bin/RefMapOpt.sh
-bin/ReferenceOpt.hyb.sh
 bin/ReferenceOpt.sh
 bin/Rename_SequenceFiles.sh
 bin/Rename_for_dDocent.sh
diff --git a/ddocent/TODO b/ddocent/TODO
new file mode 100644
index 0000000000..5cbd98a0e4
--- /dev/null
+++ b/ddocent/TODO
@@ -0,0 +1,2 @@
+- Look into ddocent-test not working
+- Update deps as needed
diff --git a/ddocent/distinfo b/ddocent/distinfo
index 7503da456f..59ae261456 100644
--- a/ddocent/distinfo
+++ b/ddocent/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-SHA1 (dDocent-2.2.25.tar.gz) = 5bdb9419a7d6770114d1bb363fcf1af07d49190b
-RMD160 (dDocent-2.2.25.tar.gz) = a33107f9d3269f647f9970b0bfcd14e15bca9575
-SHA512 (dDocent-2.2.25.tar.gz) = d7ba86d363b50dba648bb7b26e4e3c0306b3b5735e9cdea95a8d00164e12649781f325ae3fe8fba14ed76fa6478ecdf3263b07002cd8df3067fb0359e657765a
-Size (dDocent-2.2.25.tar.gz) = 336804 bytes
-SHA1 (patch-dDocent) = fbb7e5fdb7dbd5121b8ba1394cf324ffa2577778
+SHA1 (dDocent-2.5.2.tar.gz) = a78fb0496cedca4d5b3ed72e06a941a17b798d4f
+RMD160 (dDocent-2.5.2.tar.gz) = 7b695470f00c0458a8e774a25f58348a34fe2967
+SHA512 (dDocent-2.5.2.tar.gz) = 8c9c756ce0ce4c2986f99eccf7d8676c588e081b21bf0a5669325ebad13305a5f3b077a449155456a7c761e13a968e39acf056a17b3ed5a94095bd732a2b7ac8
+Size (dDocent-2.5.2.tar.gz) = 341990 bytes
+SHA1 (patch-dDocent) = c3486378d46f1e08c6a8688139f1d21fed232dae
diff --git a/ddocent/patches/patch-dDocent b/ddocent/patches/patch-dDocent
index a4bc2c8ab5..98caaedf0f 100644
--- a/ddocent/patches/patch-dDocent
+++ b/ddocent/patches/patch-dDocent
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Use pkgsrc trimmomatic path, support additional platforms
 
---- dDocent.orig	2017-11-29 17:09:13.000000000 +0000
+--- dDocent.orig	2018-06-11 21:47:49.000000000 +0000
 +++ dDocent
 @@ -1,6 +1,9 @@
  #!/usr/bin/env bash
@@ -12,7 +12,7 @@ $NetBSD$
 +export SHELL=%%PREFIX%%/bin/bash
 +
  ##########dDocent##########
- VERSION='2.2.25'
+ 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.
 @@ -27,15 +30,15 @@ do
  	fi
@@ -34,15 +34,15 @@ $NetBSD$
  	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         	
+@@ -87,6 +90,7 @@ SEQTK=( `seqtk 2>&1  | grep Version | cu
+ 	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 '
+@@ -96,7 +100,7 @@ VCFTV=$(vcftools | grep VCF | grep -oh '
          elif [ "$VCFTV" -ge "12" ]; then
                  VCFGTFLAG="--max-missing"
  	fi
@@ -51,7 +51,7 @@ $NetBSD$
  	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"
-@@ -107,7 +111,7 @@ BTC=$( bedtools --version | mawk '{print
+@@ -114,7 +118,7 @@ BTC=$( bedtools --version | mawk '{print
  		exit 1	
  	fi
  		
@@ -60,32 +60,45 @@ $NetBSD$
           awk=gawk
      else
           awk=awk
-@@ -388,10 +392,10 @@ if [ "$SNP" != "no" ]; then
- 	}
- 	export -f call_genos
+@@ -440,7 +444,7 @@ if [ "$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"
+ 
  
--	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 $FB1 --no-notice "samtools view -b -L mapped.{}.bed | freebayes -c -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10"
+ 	if [ -f "freebayes.error" ]; then
+@@ -467,7 +471,7 @@ if [ "$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
+@@ -492,7 +496,7 @@ 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
  
- 	rm mapped.*.bed 
-@@ -447,8 +451,8 @@ fi
+ 	if [ -f "freebayes.error" ]; then
+@@ -560,8 +564,8 @@ fi
  
  #Function for trimming reads using trimmomatic
  trim_reads(){
 -	TRIMMOMATIC=$(find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | head -1)
--    ADAPTERS=$(find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | head -1)
-+       TRIMMOMATIC=%%JAVAJARDIR%%/trimmomatic.jar
-+       ADAPTERS=%%PREFIX%%/share/trimmomatic/adapters/TruSeq2-PE.fa
+-    	ADAPTERS=$(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 +751,14 @@ else
+@@ -1028,7 +1032,14 @@ else
  fi
  
  #Tries to get number of processors, if not asks user
@@ -101,20 +114,20 @@ $NetBSD$
  NUMProc=$(($NUMProc + 0)) 
  
  echo "dDocent detects $NUMProc processors available on this system."
-@@ -764,7 +775,15 @@ if [ $NUMProc -lt 1 ]; then
+@@ -1045,7 +1056,15 @@ 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))G
+-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
++	MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))G
 +elif [ `uname` = FreeBSD ]; then
-+    MAXMemory=`sysctl -n hw.realmem`
-+    MAXMemory=$((MAXMemory / 1073741824))G
++	MAXMemory=`sysctl -n hw.realmem`
++	MAXMemory=$((MAXMemory / 1073741824))G
 +else
-+    printf "Unsupported platform: `uname`\n"
-+    exit 1
++	printf "Unsupported platform: `uname`\n"
++	exit 1
 +fi
  
- 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 
+ 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"
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