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-rw-r--r--INSTALL.md15
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py4
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")