--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts/run-mummer1.csh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,26 @@
+#!__CSH_PATH -f
+#
+# **SEVERELY** antiquated script for running the mummer 1 suite
+# -r option reverse complements the query sequence, coordinates of the reverse
+# matches will be relative to the reversed sequence
+#
+
+set ref = $1
+set qry = $2
+set pfx = $3
+set rev = $4
+
+set bindir = __BIN_DIR
+
+if($ref == '' || $qry == '' || $pfx == '') then
+    echo "USAGE: $0 <fasta reference> <fasta query> <prefix> [-r]"
+    exit(-1)
+endif
+
+echo "Find MUMs"
+$bindir/mummer -mum -l 20 $rev $ref $qry | tail +2 > $pfx.out
+echo "Determine gaps"
+$bindir/gaps $ref $rev < $pfx.out > $pfx.gaps
+echo "Align gaps"
+$bindir/annotate $pfx.gaps $qry > $pfx.align
+mv witherrors.gaps $pfx.errorsgaps