From 3736bd0044ddee68180a06809847af7542951743 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 19 Apr 2015 09:46:15 +0200
Subject: INSTALL info

---
 INSTALL.md                            | 15 ++++++++++++---
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py |  4 ++--
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index 38d15090..afe22678 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -1,5 +1,10 @@
 # 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
@@ -10,12 +15,14 @@ Clone the repository (currently ~800Mb) to local
 
 GN2 requires
 
+* python
 * redis
 * mysql
 
 ## Required python modules
 
-Install the following python modules:
+Install the following python modules (it is probably wise to use a local
+Python with environment for this)
 
 * Flask
 * pyyaml
@@ -53,12 +60,14 @@ 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
+$python ./runserver.py
 
 or
 
-python ./secure_server.py
+$python ./secure_server.py
 ```
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index b2067b27..98bbead8 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -856,7 +856,7 @@ def gwas_with_redis(key,species,new_code=True):
         print(key)
         v = params[key]
         if v is not None:
-            v = np.array(v)
+            v = np.array(v).astype(np.float)
         return v
 
     def narrayT(key):
@@ -969,6 +969,6 @@ if __name__ == '__main__':
     if has_gn2:
         gn2_main()
     else:
-        print("Run from runlmm.py instead")
+        fatal("Run from runlmm.py instead")
 
 
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