Create a script that executes the pipeline

generation.sh

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+usage() {
+	echo "usage: generation.sh <number of sequences>"
+	exit 1
+}
+
+if [ $# != 1 ]; then
+	usage
+fi
+
+sequences=$1
+data_directory="data/"
+prefix="curesim_"
+
+Rscript src/repertoire.r "$sequences"
+
+for file in "$data_directory"*.fastq; do
+	file_name=$(echo "$file" | cut -d / -f 2)
+	java -jar tools/CuReSim.jar -f "$file" -o "$data_directory$prefix$file_name"
+done