From b51706d0c0fa5ee0810df48f184c498b738e3c3e Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Fri, 26 Feb 2021 02:59:22 +0100
Subject: [PATCH] Create a script that executes the pipeline

---
 generation.sh | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100755 generation.sh

diff --git a/generation.sh b/generation.sh
new file mode 100755
index 0000000..10a47bc
--- /dev/null
+++ b/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