phewas: preparing for use of phewas tools

3 files changed, 16 insertions, 6 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 52d3155c..ff1146b6 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,5 +1,11 @@
 #! /bin/bash
 #
+# Typical usage
+#
+#   env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2
+#
+# Where GN2_PROFILE points to the GNU Guix profile used for deployment.
+#
 # This will run the GN2 server (with default settings if none
 # supplied). Pass in your own settings file, e.g.
 #
@@ -106,6 +112,9 @@ echo -n "dir $TMPDIR
 dbfilename gn2.rdb
 " | redis-server - &
 
+# Overrides for packages that are not yet public (currently r-auwerx)
+export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
+
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
 echo "Starting with $settings"
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..671657e8 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -328,7 +328,7 @@ class DatasetGroup(object):
         if check_plink_gemma():
             marker_class = HumanMarkers
         else:
-            marker_class = Markers            
+            marker_class = Markers
 
         self.markers = marker_class(self.name)
 
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index adacc712..40616223 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -19,16 +19,17 @@ ENDC  = '\033[0m'
 import os
 app.config['SECRET_KEY'] = os.urandom(24)
 
-from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting
+from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool
 
 port = get_setting_int("SERVER_PORT")
 
 print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
 
-import requests
-page = requests.get(get_setting("GN_SERVER_URL"))
-if page.status_code != 200:
-    raise Exception("API server not found!")
+if get_setting_bool("USE_GN_SERVER"):
+    import requests
+    page = requests.get(get_setting("GN_SERVER_URL"))
+    if page.status_code != 200:
+        raise Exception("API server not found!")
 
 print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))