Updated docs

Author: husensofteng

README.md

@@ -1,2 +1,22 @@
 # regdriver
-regDriver detect functional somatic mutaionts
+regDriver to detect functional somatic mutaionts
+
+## Required tools and modules
+
+The following packages are required to run the regDriver method:
+- Python 2.7: we recommend installing it from anaconda.com
+- bedtools v25.9
+- pybedtools (v0.7.8): for processing the annotation data files (e.g. conda install pybedtools=0.7.8 -c bioconda)
+- The following python packages are also required to run the helper modules:
+	- requests
+	- userlib 
+	- numpy
+	
+
+## Run the regDriver
+
+	```python regDriver.py regDriver_params.conf```
+
+
+	A copy of the regDriver_params.conf file that contains all parameters and options for the file can be found above 
+

regDriver.py

@@ -20,7 +20,8 @@
 import shutil
 
 def usage():
-    return "***Usage***\n python regDriver.py [param=value] regDriver_params.conf_file (priority is given to the command line arguments then the input params file"
+    print("***Usage***\n python regDriver.py [param=value] regDriver_params.conf_file (priority is given to the command line arguments then the input params file)")
+    sys.exit(0)
 
 def map_cellNames_to_originTypes(originType_cell_dict_input_file):
 
@@ -459,11 +460,10 @@ def get_value(str):
 if __name__ == '__main__':
 
     params = get_params(sys.argv)
-    print("Given params")
-    print(params)
     if len(params.keys())==0:
         usage()
-        sys.exit(0)
+    print("Given params", params)
+        
     run_training = get_value(params['run_training_arg'])    
     take_abs_entropy_diff = get_value(params['take_abs_entropy_diff_arg'])
     use_gene_expression_for_scoring = get_value(params['use_gene_expression_for_scoring_arg'])