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Installation for RedHat Enterprise Linux Server 6.3

System Setup

Yum Development Tools

sudo yum groupinstall -y 'Development Tools'

devuser

sudo /usr/sbin/adduser devuser -m
sudo chmod 770 /home/devuser
sudo chmod g+s /home/devuser
sudo mkdir -p /home/devuser/webapps

nginx

echo '[nginx]
name=nginx repo
baseurl=http://nginx.org/packages/rhel/6/$basearch/
gpgcheck=0
enabled=1' | sudo tee /etc/yum.repos.d/nginx.repo

sudo yum install -y nginx
sudo /etc/init.d/nginx start
sudo /sbin/chkconfig --levels 2345 nginx on
sudo /usr/sbin/usermod -aG devuser nginx

SSL Certs

Assuming SSL certs are available. Replace the <...> variables with the paths to the appropriate files.

sudo mkdir -p /etc/nginx/ssl
sudo mv <ssl_cert.pem> <ssl_cert.key> /etc/nginx/ssl

echo 'server {
    listen       443 default ssl;
    server_name  _;

    ssl                         on;
    ssl_certificate             ssl/<ssl_cert.pem>;
    ssl_certificate_key         ssl/<ssl_cert.key>;

    ssl_protocols  SSLv2 SSLv3 TLSv1;
    ssl_ciphers  HIGH:!aNULL:!MD5;
    ssl_prefer_server_ciphers   on;

    ssl_session_timeout  5m;

    location / {
        root   /usr/share/nginx/html;
        index  index.html index.htm;
    }
}' | sudo tee /etc/nginx/conf.d/ssl.conf

Add iptables entry

If SSL is used, replace <PORT> with 443, otherwise 80.

sudo iptables -A INPUT -m state --state NEW -m tcp -p tcp --dport <PORT> -j ACCEPT
sudo /sbin/service iptables save
sudo /sbin/service iptables restart

Python

sudo yum install -y bzip2-devel readline-devel sqlite-devel zlib-devel openssl-devel tk-devel

wget http://python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2
tar jxf Python-2.7.3.tar.bz2 && cd Python-2.7.3
./configure --enable-shared
make
sudo make altinstall

echo '/usr/local/lib' | sudo tee -a /etc/ld.so.conf
sudo /sbin/ldconfig

Base Packages

curl http://python-distribute.org/distribute_setup.py | sudo /usr/local/bin/python2.7
curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py | sudo /usr/local/bin/python2.7
sudo pip install virtualenv

Supervisor

sudo pip install supervisor
sudo /usr/sbin/groupadd supervisor

echo '#!/bin/bash
#
# Startup script for the Supervisor server
#
# Tested with Red Hat Enterprise Linux Server release 5.5
#
# chkconfig: 2345 85 15
# description: Supervisor is a client/server system that allows its users to \
#              monitor and control a number of processes on UNIX-like \
#              operating systems.
#
# processname: supervisord
# pidfile: /var/run/supervisord.pid

# Source function library.
. /etc/rc.d/init.d/functions

RETVAL=0
prog="supervisord"
SUPERVISORD=/usr/local/bin/supervisord
CONFIG_FILE=/etc/supervisord.conf
PID_FILE=/var/run/supervisord.pid

start()
{
        echo -n $"Starting $prog: "
        $SUPERVISORD --configuration $CONFIG_FILE --pidfile $PID_FILE && success || failure
        RETVAL=$?
        echo
        return $RETVAL
}

stop()
{
        echo -n $"Stopping $prog: "
        killproc -p $PID_FILE -d 10 $SUPERVISORD
        RETVAL=$?
        echo
}

reload()
{
        echo -n $"Reloading $prog: "
        if [ -n "`pidfileofproc $SUPERVISORD`" ] ; then
            killproc $SUPERVISORD -HUP
        else
            # Fails if the pid file does not exist BEFORE the reload
            failure $"Reloading $prog"
        fi
        sleep 1
        if [ ! -e $PID_FILE ] ; then
            # Fails if the pid file does not exist AFTER the reload
            failure $"Reloading $prog"
        fi
        RETVAL=$?
        echo
}

case "$1" in
        start)
                start
                ;;
        stop)
                stop
                ;;
        restart)
                stop
                start
                ;;
        reload)
                reload
                ;;
        status)
                status -p $PID_FILE $SUPERVISORD
                RETVAL=$?
                ;;
        *)
                echo $"Usage: $0 {start|stop|restart|reload|status}"
                RETVAL=1
esac
exit $RETVAL' | sudo tee /etc/init.d/supervisord

chmod +x /etc/init.d/supervisord
sudo /sbin/chkconfig --add supervisord
sudo /sbin/chkconfig --level 2345 supervisord on

sudo mkdir -p /etc/supervisor.d /var/log/supervisor

echo '[unix_http_server]
file=/tmp/supervisor.sock
chmod=0770
chown=nobody:supervisor

[supervisord]
logfile=/var/log/supervisor/supervisord.log
childlogdir=/var/log/supervisor

[rpcinterface:supervisor]
supervisor.rpcinterface_factory = supervisor.rpcinterface:make_main_rpcinterface

[supervisorctl]
serverurl=unix:///tmp/supervisor.sock

[include]
files = /etc/supervisor.d/*.ini' | sudo tee /etc/supervisord.conf

Memcache

sudo yum install -y memcached
sudo /etc/init.d/memcached start
sudo /sbin/chkconfig --level 2345 memcached on

Ruby

sudo yum install -y ruby

Ruby Gems

wget http://production.cf.rubygems.org/rubygems/rubygems-1.8.24.tgz
tar zxf rubygems-1.8.24.tgz
cd rubygems-1.8.24 && sudo ruby setup.rb

Gems

sudo gem install sass bourbon

NodeJS

wget http://nodejs.org/dist/v0.8.14/node-v0.8.14.tar.gz
tar zxf node-v0.8.14.tar.gz
cd node-v0.8.14
./configure
make
sudo make install

Node Libraries

sudo npm install -g coffee-script

PostgreSQL

It is highly recommended a separate VM is used for hosting the database server.

echo '[postgresql]
name=Official PostgreSQL Repo
baseurl=http://yum.postgresql.org/9.2/redhat/rhel-6-x86_64/
gpgcheck=0
enabled=1' | sudo tee /etc/yum.repos.d/postgresql.repo

sudo yum install -y postgresql92 postgresql92-libs postgresql92-devel
sudo /etc/init.d/postgresql-9.2 initdb
sudo /etc/init.d/postgresql-9.2 start

TODO programmatic commands for creating the database and user

echo 'export PATH=/usr/pgsql-9.2/bin:$PATH' | sudo tee /etc/profile.d/postgres.sh

Redis

sudo yum install -y redis
sudo /etc/init.d/redis start
sudo /sbin/chkconfig --levels 2345 redis on

Scala

This is only required for to perform HGMD ETL.

echo '[typesafe]
name=Typesafe Rpm Repository
baseurl=http://rpm.typesafe.com/
gpgcheck=0
enabled=1' | sudo tee /etc/yum.repos.d/typesafe.repo

sudo yum install -y scala java-1.7.0-openjdk

Deployment

The simplest way to deploy Varify is to use the supplied deploy Fabric command. Your user on the remote machine must have permission to perform the various deployment tasks. This currently includes being in the devuser and supervisor Unix groups (these were created above).

Follow the steps below to deploy to a remote host.

Clone Varify locally

git clone https://github.com/cbmi/varify.git

Install Fabric

This must version 1.4.x since 1.5+ is broken at the time of this writing. This can of course be done in a virtual environment as well to not pollute your system site-packages.

pip install fabric

Deploy

Deploy to a particular host such as production on a given branch and commit SHA1 (or tag). The branch is optional, however the commit is not, this is by design to prevent deploying the wrong commit.

fab -H <HOST> deploy:<BRANCH>@<COMMIT>

Adding Hosts

The .fabhosts file contains target environments which define the deployment and environment variables such as the hostname, paths, etc. Unless a new host is being added, this file does not need to be modified.

Config files

There are four files that need to be added to support a new host. Each are named after the host, e.g. production.

  • settings/<HOST>.py
  • server/nginx/<HOST>.conf
  • server/uwsgi/<HOST>.ini
  • server/supervisor/<HOST>.ini

The fabfile.py commands move these files to the specific locations on the remote host. Read more by running:

python -c 'import fabfile;help(fabfile)'