#!/usr/bin/env bash
#this srcipt is to do wheat_bsa
#author lee
#this is fail test, because bash didn't care about the failure of command
#this can prevent the situation that check result of each step, only right can go on
set -Eeuo pipefail
#display for better use and record log of change
Usage(){
cat <<EOF
Usage:
$0 Input: Gene ID
$0 Haplotype
$0 Phenotype
$0 -h (help) (Display this document)
EOF
exit 1
}
Usage
#basename:basename---strip directory and suffix from filenames
#dirname:---keep directory only cd `dirname $0` can change the work directory and perform command
### index
OUTPUT_DIR=/public/home/caisl/lee/my_rnaseq/rna
mkdir -p "$OUTPUT_DIR"
LOG_DIR=/public/home/caisl/lee/my_rnaseq/rna/log
mkdir -p "$LOG_DIR"
ref_seq=/public/home/caisl/lee/my_rnaseq/Triticum_aestivum.IWGSC.dna.toplevel.fa
annotation=/public/home/caisl/lee/my_rnaseq/Triticum_aestivum.IWGSC.51.gtf
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