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 ============================================ 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 ========================================== 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 ===========================================