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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/run-mummer1 @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #! -f
2 #
3 # **SEVERELY** antiquated script for running the mummer 1 suite
4 # -r option reverse complements the query sequence, coordinates of the reverse
5 # matches will be relative to the reversed sequence
6 #
7
8 set ref = $1
9 set qry = $2
10 set pfx = $3
11 set rev = $4
12
13 set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
14
15 if($ref == '' || $qry == '' || $pfx == '') then
16 echo "USAGE: $0 <fasta reference> <fasta query> <prefix> [-r]"
17 exit(-1)
18 endif
19
20 echo "Find MUMs"
21 $bindir/mummer -mum -l 20 $rev $ref $qry | tail +2 > $pfx.out
22 echo "Determine gaps"
23 $bindir/gaps $ref $rev < $pfx.out > $pfx.gaps
24 echo "Align gaps"
25 $bindir/annotate $pfx.gaps $qry > $pfx.align
26 mv witherrors.gaps $pfx.errorsgaps