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biology/ddocent/files/patch-dDocent

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PropertyOld ValueNew Value
fbsd:nokeywordsnullyes
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svn:eol-stylenullnative
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svn:mime-typenulltext/plain
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--- dDocent.orig 2018-04-20 00:10:34 UTC
+++ dDocent
@@ -1,6 +1,9 @@
#!/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
-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 '
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
-
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 $FB1 --no-notice "samtools view -b -L mapped.{}.bed | freebayes -c -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10"
rm mapped.*.bed
@@ -447,8 +450,8 @@ fi
#Function for trimming reads using trimmomatic
trim_reads(){
- TRIMMOMATIC=$(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 &> $1.trim.log
@@ -747,7 +750,14 @@ else
fi
#Tries to get number of processors, if not asks user
-NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` )
+if [ `uname` = Linux ]; then
+ NUMProc=( `grep -c ^processor /proc/cpuinfo 2> /dev/null` )
+elif [ `uname` = FreeBSD ]; then
+ NUMProc=( `sysctl -n hw.ncpu` )
+else
+ printf "Unsupported platform: `uname`\n"
+ exit 1
+fi
NUMProc=$(($NUMProc + 0))
echo "dDocent detects $NUMProc processors available on this system."
@@ -764,7 +774,15 @@ if [ $NUMProc -lt 1 ]; then
fi
#Tries to get maximum system memory, if not asks user
-MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))G
+if [ `uname` = Linux ]; then
+ MAXMemory=$(($(grep -Po '(?<=^MemTotal:)\s*[0-9]+' /proc/meminfo | tr -d " ") / 1048576))G
+elif [ `uname` = FreeBSD ]; then
+ MAXMemory=`sysctl -n hw.realmem`
+ MAXMemory=$((MAXMemory / 1073741824))G
+else
+ printf "Unsupported platform: `uname`\n"
+ exit 1
+fi
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