diff options
Diffstat (limited to 'INSTALL.md')
| -rw-r--r-- | INSTALL.md | 49 |
1 files changed, 18 insertions, 31 deletions
@@ -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 |