Mercurial > repos > rliterman > csp2
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 |
parents | |
children |
line wrap: on
line source
#! -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