add lock

2 files changed, 30 insertions, 1 deletions

diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index e778cbd..f6269d5 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -27,6 +27,7 @@ check_mers() {
 	fi
 
 	# check each mer size and process if not already run
+	lock $tmp_directory/counts-lock
 	for (( mer = min_mer_range; mer <= max_mer_range; mer++)) ; do 
 		if [[ ! -e "$counts"-counts-"$mer" ]]; then
 			echo "    checking $mer mers for $fasta_file"
@@ -39,7 +40,7 @@ check_mers() {
 		cat "$counts"-counts-"$mer" >> "$counts"-counts
 
 	done
-
+	rmdir $tmp_directory/counts-lock
 }
 
 all=run
diff --git a/src/lock b/src/lock
new file mode 100644
index 0000000..22191fe
--- /dev/null
+++ b/src/lock
@@ -0,0 +1,28 @@
+lock() {
+
+	if [[ -f "$1" ]]; then
+		echo "$1 is not a lock directory."
+		exit 1
+	fi
+
+	if mkdir "$1" &>/dev/null;  then
+		echo "lock $1 created" >&2
+	else
+		echo "lock $1 found, waiting for unlock" >&2
+		while true; do
+			sleep 2;
+			if [[ ! -d "$1" ]]; then
+				return
+			fi
+		done
+	fi;
+
+}
+
+if [[ "$#" -eq "1" ]]; then
+	lock "$1"
+else
+	echo "please supply one argument: the lock directory."
+	exit 1
+fi
+