From f755e7d4b478e8acc9613d663e40c2a0aca7c18f Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 12:53:30 +0000
Subject: Update INSTALL.md

---
 INSTALL.md | 49 ++++++++++++++++++-------------------------------
 1 file changed, 18 insertions(+), 31 deletions(-)

(limited to 'INSTALL.md')

diff --git a/INSTALL.md b/INSTALL.md
index 3ef2d5b3..3e6d2f02 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -1,17 +1,25 @@
 # INSTALL Genenetwork2 (GN2)
 
+## Guix installs
+
+The recommended way of installing GN2 is through GNU Guix.
+
 ## Use a Docker image
 
 A Docker image can be generated from
 [here](https://github.com/lomereiter/gn2-docker).
 
-## Fetch GN2 from github
+(no longer up-to-date).
+
+## Install GN2 from source
+
+Currently a difficult exercise. More information coming soon.
 
 Clone the repository (currently ~800Mb) to local
 
     git clone git@github.com:genenetwork2/genenetwork2.git
 
-## Dependencies
+### Dependencies
 
 GN2 requires
 
@@ -19,7 +27,7 @@ GN2 requires
 * redis-server
 * mysql-server
 
-## Required python modules
+### Required python modules
 
 Install the following python modules (it is probably wise to use a local
 Python with environment for this)
@@ -32,19 +40,21 @@ Python with environment for this)
 * pp
 * Flask-SQLAlchemy
 
-## Set up local file settings.py
+(not complete)
+
+### 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
+ #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
+ # http://pythonhosted.org/Flask-Security/configuration.html
 SECURITY_CONFIRMABLE = True
 SECURITY_TRACKABLE = True
 SECURITY_REGISTERABLE = True
@@ -59,30 +69,7 @@ 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'
+(not complete)
 
 ## Other information
 
-- 
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