--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/examples/run_example.sh	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,26 @@
+#/bin/bash
+include ../bin/rdiff_config.sh
+
+set -e 
+
+echo
+echo ${PROG}: This program is part of the rDiff version $RDIFF_VERSION.
+echo
+echo rDiff performs differential expression testing from RNA-Seq measurements.
+echo
+
+if [ -z "$1" -o "$1" == '--help' ];
+then
+echo Usage: $0 poisson\|param\|nonparam
+  echo " or:" $0 --help
+  false
+fi
+if [ "$1" != 'poisson' -a "$1" != 'param' -a "$1" != 'nonparam' ];
+then
+echo invalid parameter: $1
+  false
+fi
+
+
+
+../bin/rdiff -o results -d data/ -a example_condition_A_replicate_1.bam,example_condition_A_replicate_2.bam -b example_condition_B_replicate_1.bam,example_condition_B_replicate_2.bam -g data/genes_example.gff3 -m $1