Config-file_Portable_MyLinux.txt

#########Configuration file for andalousian-map_Portable.sh for test sample mf76_sub

###Analysis test1_MyLinux_2017-03-01
##F. BESNARD
##Run on MyLinux (rdp-640-fb)

##Sample mf76_sub
#test subsample, random subset of higher sequencing data

########################
## Your setup config  ##
########################
#Path to the andalousian-mapping folder (do not end with a /):
ANDALOUSIAN_FOLDER=/home/fabfab/softwares/andalousian-mapping/Portable

#Path to the programs used (Version software= June 2016)
#GATK (version: 3.7+)
GATKHOME=/home/fabfab/softwares/GATK/v3.7
#picard (Version: 2.3.0+)
PICARD=/home/fabfab/softwares/picard-2.9.0/picard.jar 
#snpEff (4.1+)
snpEff=/home/fabfab/softwares/snpEff
snpEff_config=/home/fabfab/softwares/andalousian-mapping/Portable/data/snpEff-Databases/snpEff_andalousian.config
snpEff_database=O.tipulae.2.0

#Memory of the java programs (-Xmx${RAM}g option)
RAM=12 

########################
##    Your Inputs     ##
########################
#Reference genome
REFERENCE=/home/fabfab/softwares/andalousian-mapping/Portable/data/Reference_genomes/Otipulae/nOt.2.0/nOt.2.0.fna

#Sequencing Reads 
#if several Runs:
NbRUNS=1

declare -A READS 
READS[1]=/home/fabfab/softwares/andalousian-mapping/Portable/data/sample/mf76_1_sub.fastq.gz
#/home/fabfab/Bureau/temp_PSMN/Nematodes/FabFab_Oscheius_2015-11/mf76/mf76_1.fq.gz
READS[2]=/home/fabfab/softwares/andalousian-mapping/Portable/data/sample/mf76_2_sub.fastq.gz
#/home/fabfab/Bureau/temp_PSMN/Nematodes/FabFab_Oscheius_2015-11/mf76/mf76_2.fq.gz

RGPL=ILLUMINA 
RGSM=mf76
RGLB=mf76_LB1
declare -A RGID
declare -A RGPU
RGID[1]=FCH3LFLBBXX_mf76
RGPU[1]=FCH3LFLBBXX_L5_mf76

#DATA required for mapping by sequencing:
#a dbSNP of the mapping strain
dbSNP=dbSNP_JU170_v2.0.vcf 
#List of scaffolds ID and their size:
Scaff_size=nOt.2.0_Scaff-size.tsv
#"Invariant" Scaffolds 
Invariant_Scaff=JU170_InvariantScaffold.interval_list
#Warning Scaffolds: list of scaffolds you want to test even if they are not linked to your mutation. (e.g. False-positive or so-far-unlinked scaffolds)
Warning_Scaff=JU170_FalsePositiveScaffold.list
#Control gVCFs:
Background_gVCF=CEW1.gVCF.vcf
Mapping_gVCF=JU170.gVCF.vcf
#Background strain ID. 
Background_strain=CEW1
#Mapping strain ID.
Mapping_strain=JU170

##Your Outputs
OUTPUT_NAME=mf76

##Screen preferences
#Color of the messages indicating script progression
col='\e[1;32m'
NC='\e[0m'