diff -Nru pepnovo-3.1.2010225/debian/changelog pepnovo-3.1.2010225/debian/changelog
--- pepnovo-3.1.2010225/debian/changelog	2010-09-01 21:04:52.000000000 +0100
+++ pepnovo-3.1.2010225/debian/changelog	2010-09-02 10:35:48.000000000 +0100
@@ -1,3 +1,9 @@
+pepnovo (3.1.2010225-3~lucid1) lucid; urgency=low
+
+  * fixed problem setting the model dir
+
+ --  Olivier Langella <Olivier.Langella@moulon.inra.fr>  Thu, 27 Aug 2010 10:18:51 +0200
+
 pepnovo (3.1.2010225-2~lucid1) lucid; urgency=low
 
   * build type is Release for debian package
diff -Nru pepnovo-3.1.2010225/src/AdvancedScoreModel.cpp pepnovo-3.1.2010225/src/AdvancedScoreModel.cpp
--- pepnovo-3.1.2010225/src/AdvancedScoreModel.cpp	2010-09-01 21:04:52.000000000 +0100
+++ pepnovo-3.1.2010225/src/AdvancedScoreModel.cpp	2010-09-02 10:35:48.000000000 +0100
@@ -1,6 +1,3 @@
-
-#include "config_moulon.h"
-
 #include "AllScoreModels.h"
 #include "PeptideRankScorer.h"
 #include "CumulativeSeqProb.h"
@@ -10,6 +7,7 @@
 
 
 
+
 // reads a model and all relevant files
 // the model files are assumed to be in the resource_dir
 // all this model's files are assumed to have a name <model_name>_XXXXX.txt
@@ -22,7 +20,7 @@
 
 	if (config_.get_resource_dir().length()<2)
 	{
-		config_.set_resource_dir(PEPNOVO_MODELS_DIR);
+		config_.set_resource_dir("Models");
 	}
 
 	config_.set_model_name(string(name));
diff -Nru pepnovo-3.1.2010225/src/PepNovo_main.cpp pepnovo-3.1.2010225/src/PepNovo_main.cpp
--- pepnovo-3.1.2010225/src/PepNovo_main.cpp	2010-09-01 21:04:52.000000000 +0100
+++ pepnovo-3.1.2010225/src/PepNovo_main.cpp	2010-09-02 10:35:48.000000000 +0100
@@ -31,6 +31,7 @@
 */
  
 
+#include "config_moulon.h"
 
 #include "AllScoreModels.h"
 #include "PeptideRankScorer.h" 
@@ -662,6 +663,8 @@
 	Config *config = model.get_config();
 	if (got_model_dir)
 		config->set_resource_dir(string(model_dir));
+	else
+		config->set_resource_dir(string(PEPNOVO_MODELS_DIR));
 
 	///////////////////////////////////////////////////////////////////
 	// Make input file list