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diff --git a/INSTALL.md b/INSTALL.md deleted file mode 100644 index b8c9c977..00000000 --- a/INSTALL.md +++ /dev/null @@ -1,89 +0,0 @@ -# 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 |