Added Pjotr's latest pylmm changes

Added GEMMA and necessary plink-format genotype files in gemma directory

Added the GEMMA genotype files to git LFS

Removed some unnecessary/duplicated code from interval_mapping.py

Separated GEMMA mapping code into its own file (will also do this for other methods) and fixed
and issue that caused it to not run

Added the table to the pair scan results page and wrote some code adding its attributes
to each marker object, but it still isn't working yet

1 files changed, 4 insertions, 3 deletions

diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 9d5686a9..5a76d1e2 100755
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -18,9 +18,10 @@ from wqflask import app
 #_ch = logging.StreamHandler()
 #_log.addHandler(_ch)
 
+print app.config
+
 import logging
-#from themodule import TheHandlerYouWant
-file_handler = logging.FileHandler("/tmp/flask_gn_log_danny_unsecure")
+file_handler = logging.FileHandler(app.config['LOGFILE'])
 file_handler.setLevel(logging.DEBUG)
 app.logger.addHandler(file_handler)
 
@@ -28,7 +29,7 @@ import logging_tree
 logging_tree.printout()
 
 app.run(host='0.0.0.0',
-        port=5003,
+        port=app.config['SERVER_PORT'],
         use_debugger=False,
         threaded=True,
         use_reloader=True)