--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/run-mummer3	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,28 @@
+#! -f
+#
+# for running the basic mummer 3 suite, should use nucmer instead when possible
+# to avoid the confusing reverse coordinate system of the raw programs.
+#
+# NOTE:  be warned that all reverse matches will then
+# be relative to the reverse complement of the query sequence.
+#
+# Edit this script as necessary to alter the matching and clustering values
+#
+
+set ref = $1
+set qry = $2
+set pfx = $3
+
+set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
+
+if($ref == '' || $qry == '' || $pfx == '') then
+    echo "USAGE: $0 <fasta reference> <multi-fasta query> <prefix>"
+    exit(-1)
+endif
+
+echo "Find MUMs"
+$bindir/mummer -mumreference -b -l 20 $ref $qry > $pfx.out
+echo "Determine gaps"
+$bindir/mgaps -l 100 -f .12 -s 600 < $pfx.out > $pfx.gaps
+echo "Align gaps"
+$bindir/combineMUMs -x -e .10 -W $pfx.errorsgaps $ref $qry $pfx.gaps > $pfx.align