Date: Sat, 4 May 2019 15:09:10 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r500812 - in head/biology/ddocent: . files Message-ID: <201905041509.x44F9AwT057411@repo.freebsd.org>
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Author: jwb Date: Sat May 4 15:09:10 2019 New Revision: 500812 URL: https://svnweb.freebsd.org/changeset/ports/500812 Log: biology/ddocent: Upgrade to 2.7.8 Reported by: portscout Added: head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh (contents, props changed) Modified: head/biology/ddocent/Makefile head/biology/ddocent/distinfo head/biology/ddocent/files/ddocent-assembly-test head/biology/ddocent/files/patch-dDocent head/biology/ddocent/pkg-plist Modified: head/biology/ddocent/Makefile ============================================================================== --- head/biology/ddocent/Makefile Sat May 4 13:00:03 2019 (r500811) +++ head/biology/ddocent/Makefile Sat May 4 15:09:10 2019 (r500812) @@ -1,10 +1,9 @@ # $FreeBSD$ -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 @@ -32,29 +31,21 @@ RUN_DEPENDS= unzip>=0:archivers/unzip \ 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 \ @@ -64,5 +55,13 @@ do-install: ${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> Modified: head/biology/ddocent/distinfo ============================================================================== --- head/biology/ddocent/distinfo Sat May 4 13:00:03 2019 (r500811) +++ head/biology/ddocent/distinfo Sat May 4 15:09:10 2019 (r500812) @@ -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 Modified: head/biology/ddocent/files/ddocent-assembly-test ============================================================================== --- head/biology/ddocent/files/ddocent-assembly-test Sat May 4 13:00:03 2019 (r500811) +++ head/biology/ddocent/files/ddocent-assembly-test Sat May 4 15:09:10 2019 (r500812) @@ -135,15 +135,11 @@ 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 @@ -312,20 +308,11 @@ cd-hit-est -i rainbow.fasta -o referenceRC.fasta -M 0 { 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 @@ -357,7 +344,6 @@ printf "Bonus Section: Optimize reference assemblies? 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 @@ -372,7 +358,7 @@ 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 Modified: head/biology/ddocent/files/patch-dDocent ============================================================================== --- head/biology/ddocent/files/patch-dDocent Sat May 4 13:00:03 2019 (r500811) +++ head/biology/ddocent/files/patch-dDocent Sat May 4 15:09:10 2019 (r500812) @@ -1,44 +1,13 @@ ---- 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 [ "$VCFTV" -ge "12" ]; then VCFGTFLAG="--max-missing" fi @@ -47,88 +16,58 @@ if [ "$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 Added: head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ddocent/files/patch-scripts_ReferenceOpt.sh Sat May 4 15:09:10 2019 (r500812) @@ -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" Modified: head/biology/ddocent/pkg-plist ============================================================================== --- head/biology/ddocent/pkg-plist Sat May 4 13:00:03 2019 (r500811) +++ head/biology/ddocent/pkg-plist Sat May 4 15:09:10 2019 (r500812) @@ -1,6 +1,5 @@ bin/ErrorCount.sh bin/RefMapOpt.sh -bin/ReferenceOpt.hyb.sh bin/ReferenceOpt.sh bin/Rename_SequenceFiles.sh bin/Rename_for_dDocent.sh
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