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Diffstat (limited to 'misc/gn_installation_notes.txt')
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diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt deleted file mode 100644 index 584080f7..00000000 --- a/misc/gn_installation_notes.txt +++ /dev/null @@ -1,346 +0,0 @@ -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 - -========================================== - -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 - -===========================================
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