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

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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."

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Get git:

sudo apt-get install git

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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 _______

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Create trash directory:
mkdir ~/.trash

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Using dpkg

Check which system packages are already installed:
dpkg -l | less

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Installing virtualenv:
sudo pip install virtualenv

Tell virtualenv which directory to use:
virtualenv ve27

Start up virtual environment:
source ~/ve27/bin/activate

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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++

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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/misc/requirements.txt

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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

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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

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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

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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)

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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

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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)

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Using Yolk

Install Yolk:
pip install yolk

Check packages installed in this virtual environment:
yolk -l

Checks packages that have updates available:
yolk -U

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Installing yaml

Install libyaml-dev:
sudo apt-get install libyaml-dev

Install yaml:
pip install pyyaml

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Install MySQL Client

To fix error "mysql_config not found" while installing packages with pip:
sudo apt-get install libmysqlclient-dev

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Installing R

sudo apt-get install r-base-dev

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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

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Install requests

pip install requests

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Install logging_tree

pip install logging_tree

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Install colordiff (just to make it easier to view differences in files, not necessary for GN)

sudo apt-get install colordiff

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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

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

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