added template scripts for running RACS ORG and IGR scripts as background processes

diff --git a/hpc/IGR_RACS-template.sh b/hpc/IGR_RACS-template.sh
new file mode 100644
index 0000000..bcbcf6b
--- /dev/null
+++ b/hpc/IGR_RACS-template.sh
@@ -0,0 +1,32 @@
+#!/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	\
+	$REFfile  interGENs_7-8.csv  sample.78	&
diff --git a/hpc/ORF_RACS-template.sh b/hpc/ORF_RACS-template.sh
new file mode 100644
index 0000000..b1d4182
--- /dev/null
+++ b/hpc/ORF_RACS-template.sh
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+#!/bin/bash
+#
+# Shell script template that can be used for running the ORF-RACS pipeline in a
+# set of different experiments.
+#
+# This script will run the RACS scripts in background, which is achieved by
+# including the "&" symbol at the end of each call to the RACS script.
+
+
+# define location of the RACS pipeline and script to run, in this case "countReads.sh"
+RACSscript="PATHtoRACS/core/countReads.sh"
+
+# define location of data and reference files
+dataDIR="PATHtoDATA/ExperimentA/run1"
+refsDIR="PATHtoREFS/"
+
+# specify reference and annotation files
+refsFILE="organismREFfile.gff3"
+fastaFILE="organismANNOTATIONfile_assembly.fasta"
+
+
+# run pipeline
+$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/  &
+
+# . . .
+