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