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comparison MUMmer/mummerplot_tool.sh @ 0:61f30d177448 default tip

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initial commit on Mummer toolsuite on toolshed
author eric
date Tue, 31 Mar 2015 14:19:49 +0200
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1 #!/bin/bash
2
3 ## simple bash to generate mummerplot of MATCH file
4 ##
5 ## Galaxy wrapper by Alex Bossers, CVI of Wageningen UR, Lelystad, NL
6 ## alex_dot_bossers_at_wur_dot_nl
7 ##
8 ##
9 ## needs a rename of the fixed name to something recognised by galaxy
10 ## needs cleanout of temp files
11 ##
12 ## call is mummerplot $format $in_match $out_file $cmd_extra
13 ## $0 $1 $2 $3 $4
14 ##
15 ## since mummerplot uses some deprecated syntax which can be fixed in the source
16 ## we redirect STDERR to dev/null to circumvent errorstatus in galaxy
17 ## io redirects 0=stdin 1=stdout 2=stderr to dev/null (or &-)
18
19 # Function to send error messages.
20 log_err() { echo "$@" 1>&2; }
21
22 # path to where mummer suite is installed
23 # adjust this for your machine
24 # this is the only hard coded path in the scripts
25 mum_path=""
26
27 if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then
28 log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer."
29 exit 127
30 fi
31
32 # some default options to generate a LARGE fixed PNG/POSTSCRIPT image and not an interactive one.
33
34 if [ "$1" = "png" ]; then
35 extension="png"
36 else
37 extension="ps"
38 fi
39
40 eval "$mum_path mummerplot --large --$1 $2 1>&- 2>&-"
41 if [ -f "out.$extension" ]; then
42 #conditional move to something known by galaxy
43 mv out.$extension $3
44 #remove gnuplot file
45 rm out.gp
46 fi
47
48 ## clean up
49 rm out.fplot
50 rm out.rplot
51
52 #end script