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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/misc/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
============================================
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
===========================================
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
==========================================
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=~/gene/wqflask/cfg/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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