Merge branch 'lmm' of github.com:pjotrp/genenetwork2 into lmm

2 files changed, 72 insertions, 2 deletions

diff --git a/INSTALL.md b/INSTALL.md
new file mode 100644
index 00000000..38d15090
--- /dev/null
+++ b/INSTALL.md
@@ -0,0 +1,64 @@
+# INSTALL Genenetwork2 (GN2)
+
+## Fetch GN2 from github
+
+Clone the repository (currently ~800Mb) to local
+
+    git clone git@github.com:genenetwork2/genenetwork2.git
+
+## Dependencies
+
+GN2 requires
+
+* redis
+* mysql
+
+## Required python modules
+
+Install the following python modules:
+
+* 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
+export WQFLASK_SETTINGS=$HOME/settings.py
+source /home/pjotr/ve27/bin/activate  
+cd genenetwork2/wqflask
+python ./runserver.py
+
+or
+
+python ./secure_server.py
+```
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 3b6b5d70..4312fed0 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -1,5 +1,5 @@
-# This is a converter for common LMM formats, so as to keep complexity
-# outside the main routines. 
+# This is a converter for common LMM formats, so as to keep file
+# reader complexity outside the main routines.
 
 # Copyright (C) 2015  Pjotr Prins (pjotr.prins@thebird.nl)
 #
@@ -31,6 +31,12 @@ python convertlmm.py [--plink] [--prefix out_basename] [--kinship kfile] [--phen
   Convert files for runlmm.py processing. Writes to stdout by default.
 
   try --help for more information
+
+Examples:
+
+  python ./my_pylmm/pyLMM/convertlmm.py --plink --pheno data/test_snps.132k.clean.noX.fake.phenos > test.pheno
+
+  python ./my_pylmm/pyLMM/convertlmm.py --plink --pheno data/test_snps.132k.clean.noX.fake.phenos --geno data/test_snps.132k.clean.noX > test.geno
 """
 
 # if len(args) == 0: