#!/bin/sh

##### Configuration #####
#Path of 'tasuke_bin'
SCRIPTS='/PATH/tasuke_bin/'

#Database
#mysql or oracle
BACKEND='mysql'

#Database connection
DB='database'
USER='user'
PASS='password'

#For oracle
TABLESP=''

#Directory for datasets
# 'install.sh' searches for datasets in following directories. And it set the datasets to the database.
# For example, this tool searches for VCF file in './tasuke_sample_data/variants/', when setting variants to the database.

#Datasets
DATADIR='/PATH/tasuke_sample_data/'

#This scripts searches for your reference(fasta format) files in 'DIR_FASTA'.
#Enter the fasta file name you use as reference genome.
DIR_FASTA='./reference.fasta'

#This scripts searches for '.gff' from in 'DIR_GFF'.
DIR_GFF='./'

#This scripts searches for '.vcf' from in 'DIR_VCF'.
DIR_VCF='./variants/'

#This scripts searches for '.tsv' from in 'DIR_TSV'.
DIR_TSV='./depth/'

#File format of your VCF files ['samtools' or 'gatk']
VCF_TYPE='samtools'
#########################
