Adding documentation

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diff --git a/doc/old/gn_installation_notes.txt b/doc/old/gn_installation_notes.txt
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-UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
-
-Enable UFW:
-sudo ufw enable
-Check status of UFW:
-sudo ufw status verbose
-
-Limit ssh:
-sudo ufw limit ssh
-
-Enable http, https:
-sudo ufw allow http
-sudo ufw allow https
-
-===========================================
-
-http://evilrouters.net/2011/02/18/using-etckeeper-with-git-on-ubuntu/
-
-Install etckeeper:
-sudo apt-get install etckeeper
-
-Edit /etc/etckeeper/etckeeper.conf to comment out VCS="bzr" and comment in VCS="git"
-
-Initialize repository:
-sudo etckeeper init
-
-Do initial commit:
-sudo etckeeper commit "Initial commit."
-
-===========================================
-
-Get git:
-
-sudo apt-get install git
-
-===========================================
-
-Clone code from git repository:
-git clone http://github.com/zsloan/genenetwork.git gene 
-
-Pull from branch in git repository:
-git pull origin flask(or whatever the branch is)
-
-**"apt-cache search" searches for text in the description for various packages, while
-"apt-file search" searches for files within the packages**
-
-Search for package with a specified file that can be installed with apt-get
-apt-file search _______
-
-============================================
-
-Create trash directory:
-mkdir ~/.trash
-
-============================================
-
-Using dpkg
-
-Check which system packages are already installed:
-dpkg -l | less
-
-===========================================
-
-Installing virtualenv:
-sudo pip install virtualenv
-
-Tell virtualenv which directory to use:
-virtualenv ve27
-
-Start up virtual environment:
-source ~/ve27/bin/activate
-
-===========================================
-
-Install libmysqlclient-dev (Mysql-Python dependency)
-sudo apt-get install libmysqlclient-dev
-
-Install python-dev (numpy dependency)
-sudo apt-get install python-dev
-
-Install scipy dependencies:
-sudo apt-get install libatlas-base-dev gfortran g++
-
-===========================================
-
-Install pip:
-sudo apt-get install python-pip
-
-REMEMBER TO SOURCE VE BEFORE INSTALLING 
-
-Comment out in requirements.txt:
-Reaper
-numarray
-
-Before installing from requirements.txt, install numpy separately:
-pip install numpy==1.7.0 (or whatever version we're using)
-
-Install from requirements.txt (after activating virtualenv):
-pip install -r gene/doc/requirements.txt
-
-===========================================
-
-Installing QTL Reaper
-
-wget http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb
-mv -v qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb qtlreaper-1.1.1.tar.gz
-tar xvf qtlreaper-1.1.1.tar.gz (to unzip)
-mkdir /home/zas1024/ve27/include/python2.7/Reaper
-python setup.py install
-
-===========================================
-
-Installing numarray 1.5.2
-
-wget http://downloads.sourceforge.net/project/numpy/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%2520Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload&ts=1358978306&use_mirror=superb-dca2
-mv -v numarray-1.5.2.tar.gz?r=http:%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FOld%20Numarray%2F1.5.2%2Fnumarray-1.5.2.tar.gz%2Fdownload numarray-1.5.2.tar.gz
-tar xvf numarray-1.5.2.tar.gz
-sudo python setup.py install
-
-===========================================
-
-Installing nginx
-
-sudo -s
-nginx=stable # use nginx=development for latest development version
-echo "deb http://ppa.launchpad.net/nginx/$nginx/ubuntu lucid main" > /etc/apt/sources.list.d/nginx-$nginx-lucid.list
-apt-key adv --keyserver keyserver.ubuntu.com --recv-keys C300EE8C
-apt-get update 
-apt-get install nginx
-
-Create configuration file in ~/gene/wqflask/other_config/nginx_conf/ (modeled off of the others)
-Create symbolic link to config file in /etc/nginx/sites-enabled/:
-ln -s dir_to_link_to linking_dir
-
-Run nginx:
-sudo /usr/sbin/nginx
-
-============================================
-
-Copy over zach_settings.py to /home/zas1024 directory (or whatever is home directory)
-
-export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
-
-============================================
-
-Install MySQL Server
-
-sudo apt-get install mysql-server
-
-mkdir /mnt/big
-fdisk /dev/sdb
-m: for help
-n: new partion
-...
-w: write to table and exit
-
-Start MySQL server:
-service mysql start
-
-Stop MySQL server:
-service mysql stop
-
-Change root password:
-mysql> UPDATE mysql.user SET Password=PASSWORD('your password') WHERE User='root';
-
-Setup accounts in MySQL (first need to delete anonymous/non-root accounts):
-#; use mysql;
-#; select * from user;
-#; delete from user where Host!="localhost";
-#; delete from user where User!="root";
-#; update user set Password = Password('yourpassword') where User='root';
-#; GRANT ALL ON *.* TO 'yourusername'@'%' IDENTIFIED BY 'yourpassword';
-#; select * from user;
-
-Use Percona to optimise my.cfg file:
-https://tools.percona.com/wizard
-
-To check # CPUs:
-grep -c processor /proc/cpuinfo
-
-To check memory, can use htop
-
-============================================
-
-Check RSA key:
-ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key
-
-03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2  root@penguin (RSA)
-
-============================================
-
-Installing redis server
-
-In the dls directory:
-$ wget http://redis.googlecode.com/files/redis-2.6.14.tar.gz
-$ tar xzf redis-2.6.14.tar.gz
-$ cd redis-2.6.14
-$ make
-
-Run redis (from inside redis-2.6.14 directory):
-src/redis-server
-
-For the rest of the installation instructions, refer to:
-http://redis.io/topics/quickstart
-
-To continue installation (from the README):
-
-In order to install Redis binaries into /usr/local/bin just use:
-
-    % make install
-
-Make install will just install binaries in your system, but will not configure
-init scripts and configuration files in the appropriate place. This is not
-needed if you want just to play a bit with Redis, but if you are installing
-it the proper way for a production system, we have a script doing this
-for Ubuntu and Debian systems:
-
-    % cd utils
-    % ./install_server
-
-The script will ask you a few questions and will setup everything you need
-to run Redis properly as a background daemon that will start again on
-system reboots.
-
-In the redis config file (/etc/redis/6379.conf) uncomment the following line:
-bind 127.0.0.1
-
-This is so only the local computer has access
-
-============================================
-
-Check RSA key:
-ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key
-
-03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2  root@penguin (RSA)
-
-============================================
-
-Using Yolk
-
-Install Yolk:
-pip install yolk
-
-Check packages installed in this virtual environment:
-yolk -l
-
-Checks packages that have updates available:
-yolk -U
-
-===========================================
-
-Installing yaml
-
-Install libyaml-dev:
-sudo apt-get install libyaml-dev
-
-Install yaml:
-pip install pyyaml
-
-===========================================
-
-Install MySQL Client
-
-To fix error "mysql_config not found" while installing packages with pip:
-sudo apt-get install libmysqlclient-dev
-
-===========================================
-
-Installing R
-
-sudo apt-get install r-base-dev
-
-===========================================
-
-Installing rpy2
-
-pip install rpy2
-
-===========================================
-
-Install Parallel Python (pp)
-
-wget http://www.parallelpython.com/downloads/pp/pp-1.6.3.tar.gz
-tar xvf pp-1.6.3.tar.gz
-python setup.py install
-
-==========================================
-
-Install requests
-
-pip install requests
-
-==========================================
-
-Install logging_tree
-
-pip install logging_tree
-
-==========================================
-
-Install colordiff (just to make it easier to view differences in files, not necessary for GN)
-
-sudo apt-get install colordiff
-
-==========================================
-
-Install NTP (network time protocol)
-
-sudo apt-get install ntp
-
-==========================================
-
-To get server running:
-
-!If having seemingly inexplicable problems with imports, make sure I've started the environment!
-
-Start up virtual environment:
-source ~/ve27/bin/activate==============
-
-Install requests
-
-pip install requests
-
-=======================
-
-To set WQFLASK_SETTINGS environment variable:
-export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located)
-
-To change screen environment variable (if man not working or to get color, for example):
-export TERM=screen
-
-To search for commands in history if necessary:
-history | grep "(whatever is being searched for)"
-
-Run web server:
-/usr/local/nginx/sbin/nginx
-
-Run server:
-python runserver.py
-
-===========================================
-
-To do full upgrade (as opposed to apt-get upgrade)
-sudo aptitude full-upgrade
-
-===========================================