view CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/run-mummer3 @ 69:33d812a61356

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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#! -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