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comparison deseq-hts_1.0/src/deseq_config.m @ 0:94a108763d9e draft

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deseq-hts version 1.0 wraps the DESeq 1.6.0
author vipints
date Wed, 09 May 2012 20:43:47 -0400
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children e27b4f7811c2
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-1:000000000000 0:94a108763d9e
1 function deseq_config
2 % DESEQ_CONFIG Sets a few global variables with system dependent paths.
3 %
4 %
5 % This program is free software; you can redistribute it and/or modify
6 % it under the terms of the GNU General Public License as published by
7 % the Free Software Foundation; either version 3 of the License, or
8 % (at your option) any later version.
9 %
10 % Written (W) 2009-2011 Regina Bohnert, Gunnar Raetsch
11 % Copyright (C) 2009-2011 Max Planck Society
12 %
13
14 % paths
15 global DESEQ_PATH DESEQ_SRC_PATH
16
17 % interpreter paths
18 global INTERPRETER MATLAB_BIN_PATH OCTAVE_BIN_PATH
19
20 % SAMTools path
21 global SAMTOOLS_DIR
22
23 % configuration (adapt to the user's configuration)
24 DESEQ_PATH = getenv('DESEQ_PATH');
25 DESEQ_SRC_PATH = getenv('DESEQ_SRC_PATH');
26 INTERPRETER = getenv('INTERPRETER');
27 MATLAB_BIN_PATH = getenv('MATLAB_BIN_PATH');
28 OCTAVE_BIN_PATH = getenv('OCTAVE_BIN_PATH');
29 SAMTOOLS_DIR = getenv('SAMTOOLS_DIR');
30
31 % switch off a few expected warnings
32 addpath(sprintf('%s/tools', DESEQ_PATH));
33 lserve=license;
34 if ~isequal(lserve, 'GNU General Public License'),
35 engine='matlab';
36 else
37 engine='octave';
38 end;
39 if isequal(engine, 'octave'),
40 warning('off', 'Octave:precedence-change');
41 warning('off', 'Octave:function-name-clash');
42 warning('off', '');
43 warning('off', 'Octave:num-to-str');
44 warning('off', 'Octave:function-name-clash');
45 warning('off', 'Octave:divide-by-zero');
46 warning('off', 'Octave:future-time-stamp');
47 warning('off', 'Octave:assign-as-truth-value');
48 else
49 warning('off', 'MATLAB:typeaheadBufferOverflow');
50 end
51
52 % make sure no process stops with a debug prompt
53 global g_ignore_keyboard
54 g_ignore_keyboard = 1;