added template scripts for running RACS ORG and IGR scripts as background processes
added template scripts for running RACS ORG and IGR scripts as background processes
#!/bin/bash
# Shell script template for running the IGR-RACS pipeline
#
# This script will run the RACS scripts in background
# generate sample files...
ls -1 alnExperimentA_*1*.bam alnExperimentA_*2*.bam > sample.12
ls -1 alnExperimentB_*3*.bam alnExperimentB_*4*.bam > sample.34
ls -1 alnExperimentC_*5*.bam alnExperimentC_*6*.bam > sample.56
ls -1 alnExperimentD_*7*.bam alnExperimentD_*8*.bam > sample.78
# define useful environment variables...
REFfile="PATHtoREFS/organismREFfile.gff3"
RACSscript="PATHtoRACS/core/intergenic/det-interGenes.sh"
# run RACS-intergenics
$RACSscript \
FINAL.table.ExperimentA_1_prot1-1_INPUT_S1_R1_001-ExperimentA_2_prot1-1_ChIP_S2_R1_001 \
$REFfile interGENs_1-2.csv sample.12 &
$RACSscript \
FINAL.table.ExperimentB_3_prot1-2_INPUT_S3_R1_001-ExperimentB_4_prot1-2_ChIP_S4_R1_001 \
$REFfile interGENs_3-4.csv sample.34 &
$RACSscript \
FINAL.table.ExperimentC_5_prot2_INPUT_S5_R1_001-ExperimentC_6_prot2_ChIP_S6_R1_001 \
$REFfile interGENs_5-6.csv sample.56 &
$RACSscript \
FINAL.table.ExperimentC_7_prot3_INPUT_S7_R1_001-ExperimentD_8_prot3_ChIP_S8_R1_001 \
$REFfile interGENs_7-8.csv sample.78 &