Merge branch 'master' of https://github.com/zsloan/genenetwork

Conflicts:
	misc/gn_installation_notes.txt

4 files changed, 44 insertions, 102 deletions

diff --git a/misc/requirements.txt b/misc/requirements.txt
index 0e892c05..ec02a2c2 100644
--- a/misc/requirements.txt
+++ b/misc/requirements.txt
@@ -9,7 +9,7 @@ Flask-WTF==0.8.3
 Jinja2==2.6
 MySQL-python==1.2.4
 PyYAML==3.10
-Reaper==1.0
+#Reaper==1.0
 Reindent==0.1.1
 SQLAlchemy==0.8.0
 WTForms==1.0.3
@@ -21,7 +21,7 @@ itsdangerous==0.17
 logging-tree==1.2
 logilab-astng==0.24.3
 logilab-common==0.59.1
-numarray==1.5.2
+#numarray==1.5.2
 numpy==1.7.0
 passlib==1.6.1
 pp==1.6.3
diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf
new file mode 100644
index 00000000..822556d3
--- /dev/null
+++ b/wqflask/other_config/nginx_conf/penguin.conf
@@ -0,0 +1,42 @@
+server {
+    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+    listen 80;
+
+    server_name penguin.uthsc.edu;
+
+    access_log  /var/log/nginx/access.log;
+    error_log  /var/log/nginx/error.log;
+
+    location ^~ /css/ {
+            root /gene/wqflask/wqflask/static/;
+    }
+
+    location ^~ /javascript/ {
+            root /gene/wqflask/wqflask/static/;
+    }
+
+#    location ^~ /image/ {
+#           root /gene/wqflask/wqflask/static/;
+#       }
+
+    location ^~ /images/ {
+            root /gene/wqflask/wqflask/static/;
+    }
+    
+    ### New - added by Sam
+    #location ^~ /static/ {
+    #       root /gene/wqflask/wqflask/static/;
+    #}
+
+    location / {
+            proxy_pass         http://127.0.0.1:5000/;
+            proxy_redirect     off;
+
+            proxy_set_header   Host             $host;
+            proxy_set_header   X-Real-IP        $remote_addr;
+            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
+            
+            proxy_read_timeout 40m;
+    }
+}
+
diff --git a/wqflask/other_config/wqflask-nginx.conf b/wqflask/other_config/wqflask-nginx.conf
deleted file mode 100644
index 4e6fd0d9..00000000
--- a/wqflask/other_config/wqflask-nginx.conf
+++ /dev/null
@@ -1,83 +0,0 @@
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2python.genenetwork.org;
-
-    access_log  /var/log/nginx/access.log;
-    error_log  /var/log/nginx/error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5000/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
-
-server {
-    # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
-    listen 80;
-
-    server_name gn2python_lei.genenetwork.org;
-
-    access_log  /var/log/nginx/lei_access.log;
-    error_log  /var/log/nginx/lei_error.log;
-
-    location ^~ /css/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-    location ^~ /javascript/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-
-#    location ^~ /image/ {
-#           root /gene/wqflask/wqflask/static/;
-#       }
-
-    location ^~ /images/ {
-            root /gene/wqflask/wqflask/static/;
-    }
-    
-    ### New - added by Sam
-    #location ^~ /static/ {
-    #       root /gene/wqflask/wqflask/static/;
-    #}
-
-    location / {
-            proxy_pass         http://127.0.0.1:5001/;
-            proxy_redirect     off;
-
-            proxy_set_header   Host             $host;
-            proxy_set_header   X-Real-IP        $remote_addr;
-            proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
-            
-            proxy_read_timeout 40m;
-    }
-}
diff --git a/wqflask/requirements.txt b/wqflask/requirements.txt
deleted file mode 100644
index 4449c0e7..00000000
--- a/wqflask/requirements.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-Flask==0.9
-Jinja2==2.6
-#MySQL-python==1.2.3
-Piddle==0.1-dev
-PyYAML==3.10
-SQLAlchemy==0.7.9
-Werkzeug==0.8.3
-logging-tree==1.1
-nose==1.2.1
-numpy==1.6.2
-pp==1.6.3
-requests==0.13.3
-rpy2==2.3.1
-scipy==0.11.0
-simplejson==2.6.2
-wsgiref==0.1.2
-yolk==0.4.3