Mercurial > repos > abossers > mummer_toolsuite

comparison MUMmer/mummerplot_tool.sh @ 2:479eb076cd23

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add revised mummer toolshed files to testtoolshed
author abossers
date Tue, 28 Oct 2014 16:59:33 +0100
parents
children
comparison
equal deleted inserted replaced
1:c1c38335322e 2:479eb076cd23
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