diff deseq-hts_2.0/src/deseq_config.m @ 10:2fe512c7bfdf draft

DESeq2 version 1.0.19 added to the repo

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_2.0/src/deseq_config.m	Tue Oct 08 08:15:34 2013 -0400
@@ -0,0 +1,55 @@
+function deseq_config
+% DESEQ2_CONFIG   Sets a few global variables with system dependent paths.
+%
+%
+% This program is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation; either version 3 of the License, or
+% (at your option) any later version.
+%
+% Written (W) 2009-2011 Regina Bohnert, Gunnar Raetsch
+% Copyright (C) 2009-2011 Max Planck Society
+%
+
+% paths
+global DESEQ2_PATH DESEQ2_SRC_PATH
+
+% interpreter paths
+global INTERPRETER MATLAB_BIN_PATH OCTAVE_BIN_PATH
+
+% SAMTools path
+global SAMTOOLS_DIR
+
+% configuration (adapt to the user's configuration)
+DESEQ2_PATH = getenv('DESEQ2_PATH');
+DESEQ2_SRC_PATH = getenv('DESEQ2_SRC_PATH');
+INTERPRETER = getenv('INTERPRETER');
+MATLAB_BIN_PATH = getenv('MATLAB_BIN_PATH');
+OCTAVE_BIN_PATH = getenv('OCTAVE_BIN_PATH');
+SAMTOOLS_DIR = getenv('SAMTOOLS_DIR');
+
+% switch off a few expected warnings
+addpath(sprintf('%s/tools', DESEQ2_PATH));
+engine='';
+lserve=license;
+if ~isequal(lserve, 'GNU General Public License'),
+    engine='matlab';
+else
+    engine='octave';
+end;
+if isequal(engine, 'octave'),
+  warning('off', 'Octave:precedence-change');
+  warning('off', 'Octave:function-name-clash');
+  warning('off', '');
+  warning('off', 'Octave:num-to-str');
+  warning('off', 'Octave:function-name-clash');
+  warning('off', 'Octave:divide-by-zero');
+  warning('off', 'Octave:future-time-stamp');
+  warning('off', 'Octave:assign-as-truth-value');
+else
+  warning('off', 'MATLAB:typeaheadBufferOverflow');
+end
+
+% make sure no process stops with a debug prompt
+global g_ignore_keyboard
+g_ignore_keyboard = 1;