Merge branch 'master' of https://github.com/zsloan/genenetwork2 into zsloan

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+# INSTALL Genenetwork2 (GN2)
+
+## Use a Docker image
+
+A Docker image can be generated from
+[here](https://github.com/lomereiter/gn2-docker).
+
+## Fetch GN2 from github
+
+Clone the repository (currently ~800Mb) to local
+
+    git clone git@github.com:genenetwork2/genenetwork2.git
+
+## Dependencies
+
+GN2 requires
+
+* python
+* redis-server
+* mysql-server
+
+## Required python modules
+
+Install the following python modules (it is probably wise to use a local
+Python with environment for this)
+
+* Flask
+* pyyaml
+* redis
+* qtlreaper
+* numarray
+* pp
+* Flask-SQLAlchemy
+
+## Set up local file settings.py
+
+```python
+LOGFILE = """/tmp/flask_gn_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:password@localhost/db_webqtl"""
+SQLALCHEMY_DATABASE_URI = 'mysql://gn2:password@localhost/db_webqtl'
+
+# 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 = 5051
+
+SECRET_HMAC_CODE = '*'
+```
+
+```sh
+# Use a working copy of python
+export python=$HOME/ve27/bin/python
+export WQFLASK_SETTINGS=$HOME/settings.py
+source /home/pjotr/ve27/bin/activate  
+cd genenetwork2/wqflask
+$python ./runserver.py
+
+or
+
+$python ./secure_server.py
+```
+
+## Running tools
+
+### pylmm
+
+To run pylmm check out the repository at https://github.com/genenetwork/pylmm_gn2.
+
+Next update the setting.py file to point at the tree
+
+GN2 can locate PYLMM through PYLMM_PATH in setting.py (or in ENV)
+
+    PYLMM_PATH = '/home/test/opensource/python/pylmm_gn2'
+
+## Other information
+
+Check also the ./misc/ directory for settings