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

1 files changed, 77 insertions, 0 deletions

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