2 files changed, 39 insertions, 12 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
new file mode 100644
index 00000000..3c972557
--- /dev/null
+++ b/wqflask/utility/tools.py
@@ -0,0 +1,37 @@
+# Tools/paths finder resolves external paths from settings and/or environment
+# variables
+#
+# Currently supported:
+#
+#   PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool 
+
+import os
+
+def get_setting():
+    """
+    Resolve a setting from the environment or the global settings in app.config
+    """
+    pass
+    
+def pylmm_command(default=None):
+    def get_valid_path(path):
+        if path and os.path.isfile(path+'/lmm.py'):
+            return path
+        else:
+            None
+
+    # ---- Check whether environment exists
+    path = get_valid_path(os.environ['PYLMM_PATH'])
+    # ---- Check whether setting exists
+    if not path:
+        path = get_valid_path(app.config.get('PYLMM_PATH'))
+    # ---- Check whether default exists
+    if not path:
+        path = get_valid_path(default)
+    home = get_valid_path(os.environ['HOME']+'/pylmm_gn2')
+    if not path:
+        path = get_valid_path(home)
+    if not path:
+        raise Exception('PYLMM_PATH '+home+' unknown or faulty (add PYLMM_PATH to settings.py)')
+    pylmm_command = 'python '+path+'/lmm.py'
+    return path,pylmm_command
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 999a32b8..b210173b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -36,23 +36,13 @@ from utility import webqtlUtil
 #from wqflask.marker_regression import plink_mapping
 from wqflask.marker_regression import gemma_mapping
 #from wqflask.marker_regression import rqtl_mapping
-from wqflask.my_pylmm.data import prep_data
-# from wqflask.my_pylmm.pyLMM import lmm
-# from wqflask.my_pylmm.pyLMM import input
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
-
 from utility.benchmark import Bench
+from utility.tools import pylmm_command
 
-import os
-if os.environ.get('PYLMM_PATH') is None:
-    PYLMM_PATH=app.config.get('PYLMM_PATH')
-    if PYLMM_PATH is None:
-        PYLMM_PATH=os.environ['HOME']+'/gene/wqflask/wqflask/my_pylmm/pyLMM'
-if not os.path.isfile(PYLMM_PATH+'/lmm.py'):
-    raise Exception('PYLMM_PATH '+PYLMM_PATH+' unknown or faulty')
-PYLMM_COMMAND= 'python '+PYLMM_PATH+'/lmm.py'
+PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
 
 class MarkerRegression(object):