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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
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