Merge /home/gn2/gene

2 files changed, 83 insertions, 0 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
new file mode 100644
index 00000000..0cf40265
--- /dev/null
+++ b/etc/default_settings.py
@@ -0,0 +1,29 @@
+import os
+import sys
+
+LOGFILE = "/tmp/genenetwork2.log"
+
+# This is needed because Flask turns key errors into a
+# 400 bad request response with no exception/log
+TRAP_BAD_REQUEST_ERRORS = True
+
+DB_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
+SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
+
+# http://pythonhosted.org/Flask-Security/configuration.html
+SECURITY_CONFIRMABLE = True
+SECURITY_TRACKABLE = True
+SECURITY_REGISTERABLE = True
+SECURITY_RECOVERABLE = True
+SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
+SECURITY_POST_LOGIN_VIEW = "/thank_you"
+SQLALCHEMY_POOL_RECYCLE = 3600
+
+SERVER_PORT = 5003
+SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
+
+# Path overrides for Genenetwork
+GENENETWORK_FILES = os.environ['HOME']+"/gn2_data"
+PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
+PLINK_COMMAND = str.strip(os.popen("which plink2").read())
+GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
diff --git a/etc/nginx-genenetwork.conf b/etc/nginx-genenetwork.conf
new file mode 100644
index 00000000..06fd3c57
--- /dev/null
+++ b/etc/nginx-genenetwork.conf
@@ -0,0 +1,54 @@
+user  nobody;
+worker_processes  4;
+pid /var/run/nginx.pid;
+
+error_log  /var/log/nginx/error.log;
+
+events {
+    worker_connections  16;
+}
+
+http {
+    include       mime.types;
+    # default_type  application/octet-stream;
+
+    # sendfile        on;
+    keepalive_timeout  480;
+
+    server {
+        listen       80;
+        server_name  localhost;
+
+        location / {
+            root   html;
+            index  index.html index.htm;
+        }
+
+        error_page   500 502 503 504  /50x.html;
+        location = /50x.html {
+            root   html;
+        }
+    }
+
+    server {
+        listen 80;
+        server_name test-gn2.genenetwork.org;
+        access_log  logs/test-gn2.access.log;
+
+        proxy_connect_timeout       3000;
+        proxy_send_timeout          3000;
+        proxy_read_timeout          3000;
+        send_timeout                3000;
+
+        location / {
+            # proxy_set_header   Host $host;
+            proxy_set_header   Host      $http_host;
+            # proxy_redirect     off;
+            proxy_set_header   Connection keep-alive;
+            proxy_set_header   X-Real-IP $remote_addr;
+            proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
+            proxy_set_header   X-Forwarded-Host $server_name;
+            proxy_pass         http://127.0.0.1:5003;
+        }
+    }
+}