aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorpjotrp2016-02-25 12:53:30 +0000
committerPjotr Prins2016-04-20 09:46:00 +0000
commitf755e7d4b478e8acc9613d663e40c2a0aca7c18f (patch)
tree4b98b667eb61d44f23a35228fb669b64ed28b837
parentec6c3158a48a7d81596c848cb8b7f3a487bcc28a (diff)
downloadgenenetwork2-f755e7d4b478e8acc9613d663e40c2a0aca7c18f.tar.gz
Update INSTALL.md
-rw-r--r--INSTALL.md49
1 files changed, 18 insertions, 31 deletions
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