/usr/bin/run-mummer3 is in mummer 3.23+dfsg-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | #!/bin/sh -e
#
# 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
#
usage () {
echo "Usage: `basename $0` <fasta reference> <multi-fasta query> <prefix>"
return 67 # EX_USAGE
}
if [ $# -ne 3 ] ; then
echo "You provided $# arguments."
usage
fi
ref="$1"
qry="$2"
pfx="$3"
bindir=/usr/bin
if [ ! -e "$ref" ] ; then
echo "File for fasta reference $ref does not exist."
usage
fi
if [ ! -e "$qry" ] ; then
echo "File for fasta query $qry does not exist."
usage
fi
if [ "$pfx" = "" ] ; then
usage
fi
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
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