Mercurial > repos > vipints > deseq_hts
annotate 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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DESeq2 version 1.0.19 added to the repo
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1 function deseq_config |
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2 % DESEQ2_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 DESEQ2_PATH DESEQ2_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 DESEQ2_PATH = getenv('DESEQ2_PATH'); |
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25 DESEQ2_SRC_PATH = getenv('DESEQ2_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', DESEQ2_PATH)); |
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33 engine=''; |
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34 lserve=license; |
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35 if ~isequal(lserve, 'GNU General Public License'), |
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36 engine='matlab'; |
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37 else |
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38 engine='octave'; |
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39 end; |
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40 if isequal(engine, 'octave'), |
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41 warning('off', 'Octave:precedence-change'); |
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42 warning('off', 'Octave:function-name-clash'); |
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43 warning('off', ''); |
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44 warning('off', 'Octave:num-to-str'); |
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45 warning('off', 'Octave:function-name-clash'); |
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46 warning('off', 'Octave:divide-by-zero'); |
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47 warning('off', 'Octave:future-time-stamp'); |
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48 warning('off', 'Octave:assign-as-truth-value'); |
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49 else |
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50 warning('off', 'MATLAB:typeaheadBufferOverflow'); |
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51 end |
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52 |
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53 % make sure no process stops with a debug prompt |
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54 global g_ignore_keyboard |
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55 g_ignore_keyboard = 1; |