From e1cdb11c211394472e2f8cdd033fd0f93dbf5cea Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 13 Feb 2016 11:22:02 +0100
Subject: Docs: Use ./doc dir instead of ./misc

---
 INSTALL.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'INSTALL.md')

diff --git a/INSTALL.md b/INSTALL.md
index b8c9c977..3ef2d5b3 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -86,4 +86,4 @@ GN2 can locate PYLMM through PYLMM_PATH in setting.py (or in ENV)
 
 ## Other information
 
-Check also the ./misc/ directory for settings
+Check also the ./doc directory for settings
-- 
cgit v1.2.3


From f755e7d4b478e8acc9613d663e40c2a0aca7c18f Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 12:53:30 +0000
Subject: Update INSTALL.md

---
 INSTALL.md | 49 ++++++++++++++++++-------------------------------
 1 file changed, 18 insertions(+), 31 deletions(-)

(limited to 'INSTALL.md')

diff --git a/INSTALL.md b/INSTALL.md
index 3ef2d5b3..3e6d2f02 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -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
 
-- 
cgit v1.2.3


From ce07647da3b8a5411a0b9e2d3f67302594ad4aa9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 4 Mar 2016 10:19:22 +0000
Subject: Remove outdated installation instructions

---
 INSTALL.md | 76 --------------------------------------------------------------
 1 file changed, 76 deletions(-)
 delete mode 100644 INSTALL.md

(limited to 'INSTALL.md')

diff --git a/INSTALL.md b/INSTALL.md
deleted file mode 100644
index 3e6d2f02..00000000
--- a/INSTALL.md
+++ /dev/null
@@ -1,76 +0,0 @@
-# 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).
-
-(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
-
-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
-
-(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
-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 = '*'
-```
-
-(not complete)
-
-## Other information
-
-Check also the ./doc directory for settings
-- 
cgit v1.2.3