nenufaar.conf.example

#########	Set Generic interpreters  			#########

JAVA7=path/to/java7/bin/java
export JAVA_HOME=/usr/bin/
JAVA=path/to/java8/bin/java
export PATH=${JAVA_HOME}:${PATH}
echo "#############################################################################################"
echo "PATH usable by nenufaar:  ${PATH}"
echo "#############################################################################################"
####BEGIN SLURMONLY
#muse /cm devient /trinity
#module load cv-standard gcc
#LD_LIBRARY_PATH => path to lib_drmaa.so
export LD_LIBRARY_PATH=/usr/local/lib/:${LD_LIBRARY_PATH}
echo "#############################################################################################"
echo "LD_LIBRARY_PATH to use lib_drmaa for queue:  ${LD_LIBRARY_PATH}"
echo "#############################################################################################"
####END SLURMONLY
PYTHON=path/to/python
PERL=path/to/perl
BASH=path/to/bash
AWK=path/to/awk
SORT=path/to/sort

#########	Set software versions 			#########
#replace with your versions number
#version numbers can be used in path below
#e.g.
#BWA_VERSION=0.7.15
#BWA=softs/bwa/${BWA-VERSION}/bin/bwa
BWA_VERSION=0.7.15
FASTQC_VERSION=0.11.5
SAMTOOLS_VERSION=1.3.1
PICARD_VERSION=2.6.0
GATK_VERSION=3.6.0
GATK_OLD_VERSION=3.5.0
PLATYPUS_VERSION=0.8.1
QUEUE_VERSION=3.6
QUEUE_OLD_VERSION=3.5
SAMBAMBA_VERSION=0.6.3
BEDTOOLS_VERSION=2.26.0
IURC_VCF_AB_VERSION=1.0

#########	Set paths to sofware 			#########

BWA=path/to/bwa
FASTQC=path/to/fastqc
SAMTOOLS=path/to/samtools
PICARD=path/to/picard.jar
GATK=path/to/GenomeAnalysisTK.jar
#GATK old used for indel realigner (e.g. 3.5)
GATK_OLD=path/to/GenomeAnalysisTK_old_version.jar
PLATYPUS=path/to/Platypus.py
ANNOTATION_SCRIPT=nenufaar_annot.sh
VCF_POLYX=path/to/vcfpolyx.jar
QUEUE=path/to/Queue.jar
#QUEUE old used for indel realigner (e.g. 3.5)
QUEUE_OLD=path/to/Queue_old_version.jar
SAMBAMBA=path/to/sambamba_v${SAMBAMBA_VERSION}
HTSLIB=path/to/
BEDTOOLS=path/to/bin/bedtools
IURC_VCF_AB=utilities/vcf_allele_balance/vcf_allele_balance_${IURC_VCF_AB_VERSION}.pl
QUALIMAP=path/to/qualimap

#########	Set paths to data 			#########

OUTPUT_PATH=path/to/output/
SCALA_PATH=queueScripts/
#default genome is hg19
#however you can specify -g hg38 when launching nenufaar
#but in that case you must have your hg38 files in nenufaar/refData/genome/hg38/
REF_PATH=path/to/hg19.fa
SNP_PATH=path/to/CORRECT_dbsnp_138.hg19.vcf
INDEL1=path/to/1000G_phase1.indels.hg19.sites.vcf
INDEL2=path/to//Mills_and_1000G_gold_standard.indels.hg19.sites.vcf

#########	Set script options defaults 		#########

#you may change default genome here, but then you must change data paths above
GENOME=hg19
WGS=false
DCOV=1000
ANNOTATOR=0
PROTOCOL=capture
HSMETRICS=false
CALLER=hc
IP=20
STAND_EMIT_CONF=10
STAND_CALL_CONF=30
DP_THRESHOLD=20
FILTER=false
USE_PLATYPUS=true
BAM_ONLY=false
VC_ONLY=false
CLEAN_UP=true
BEDTOOLS_LOW_COVERAGE=20
BEDTOOLS_SMALL_INTERVALS=20

#########	Set computer environnment options 	#########

NB_THREAD=32
NB_NODES=1
MAX_RAM=48
MAX_RAM_GATK_SINGLE=4
PICARD_RAM=4
PARTITION=monster

#########	Set cluster commands		 	#########

SRUN_SIMPLE_COMMAND="srun --job-name=${RUN_BASEDIR_NAME}_${ID} -N${NB_NODES} -n1 -c1 --partition=${PARTITION} --mem-per-cpu=12288"
SRUN_24_COMMAND="srun --job-name=${RUN_BASEDIR_NAME}_${ID} -N${NB_NODES} -n1 -c${NB_THREAD} --partition=${PARTITION}"
QUEUE_RUNNER="-jobRunner Drmaa"

##########	Others					#########

ID=$RANDOM