From 72fb1ac4ade5b812ccafcc00076ae19dcad39b9e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 1 May 2015 22:30:00 +0000
Subject: Added Pjotr's latest pylmm changes

Added GEMMA and necessary plink-format genotype files in gemma directory

Added the GEMMA genotype files to git LFS

Removed some unnecessary/duplicated code from interval_mapping.py

Separated GEMMA mapping code into its own file (will also do this for other methods) and fixed
and issue that caused it to not run

Added the table to the pair scan results page and wrote some code adding its attributes
to each marker object, but it still isn't working yet
---
 INSTALL.md | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 INSTALL.md

(limited to 'INSTALL.md')

diff --git a/INSTALL.md b/INSTALL.md
new file mode 100644
index 00000000..9f28ac28
--- /dev/null
+++ b/INSTALL.md
@@ -0,0 +1,77 @@
+# 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
+```
+
+## Other information
+
+Check also the ./misc/ directory for settings
\ No newline at end of file
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