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 that can be used for running the ORF-RACS pipeline in a
# set of different experiments.
#
# This script will run the RACS scripts in background, which is achieved by
# including the "&" symbol at the end of each call to the RACS script.
# define location of the RACS pipeline and script to run, in this case "countReads.sh"
RACSscript="PATHtoRACS/core/countReads.sh"
# define location of data and reference files
dataDIR="PATHtoDATA/ExperimentA/run1"
refsDIR="PATHtoREFS/"
# specify reference and annotation files
refsFILE="organismREFfile.gff3"
fastaFILE="organismANNOTATIONfile_assembly.fasta"
# run pipeline
$RACSscript \
# ChIP file
$dataDIR/ExperimentA_1_prot1-1_INPUT_S1_R1_001.fastq.gz \
# INPUT file
$dataDIR/ExperimentA_2_prot1-1_ChIP_S2_R1_001.fastq.gz \
# reference files
$fastaFILE $refsDIR/$refsFILE \
# working space
/dev/shm &
$RACSscript \
$dataDIR/ExperimentA_INPUT_S2_R1.fastq.gz \
$dataDIR/ExperimentA_ChIP_S2_R1.fastq.gz \
$fastaFILE $refsDIR/$refsFILE \
/scratch1/mponce/ &
# . . .