svn commit: r500812 - in head/biology/ddocent: . files
Jason W. Bacon
jwb at FreeBSD.org
Sat May 4 15:09:12 UTC 2019
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 at 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 at 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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