Mercurial > repos > vipints > deseq_hts
comparison deseq-hts_2.0/src/deseq_config.m @ 10:2fe512c7bfdf draft
DESeq2 version 1.0.19 added to the repo
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 08:15:34 -0400 |
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9:e27b4f7811c2 | 10:2fe512c7bfdf |
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1 function deseq_config | |
2 % DESEQ2_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 DESEQ2_PATH DESEQ2_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 DESEQ2_PATH = getenv('DESEQ2_PATH'); | |
25 DESEQ2_SRC_PATH = getenv('DESEQ2_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', DESEQ2_PATH)); | |
33 engine=''; | |
34 lserve=license; | |
35 if ~isequal(lserve, 'GNU General Public License'), | |
36 engine='matlab'; | |
37 else | |
38 engine='octave'; | |
39 end; | |
40 if isequal(engine, 'octave'), | |
41 warning('off', 'Octave:precedence-change'); | |
42 warning('off', 'Octave:function-name-clash'); | |
43 warning('off', ''); | |
44 warning('off', 'Octave:num-to-str'); | |
45 warning('off', 'Octave:function-name-clash'); | |
46 warning('off', 'Octave:divide-by-zero'); | |
47 warning('off', 'Octave:future-time-stamp'); | |
48 warning('off', 'Octave:assign-as-truth-value'); | |
49 else | |
50 warning('off', 'MATLAB:typeaheadBufferOverflow'); | |
51 end | |
52 | |
53 % make sure no process stops with a debug prompt | |
54 global g_ignore_keyboard | |
55 g_ignore_keyboard = 1; |