Mutalyzer installation instructions
===================================


Default configuration notes
---------------------------

The instructions in this file are quite specific to the standard Mutalyzer
environment. This consists of a Debian stable (Squeeze) system with Apache
and Mutalyzer using its mod_wsgi module. Debian conventions are used
throughout.

The following is an overview of default locations used by Mutalyzer:

    Package files         /usr/local/lib/python2.6/dist-packages/...
    Configuration         /etc/mutalyzer/config
    Log file              /var/log/mutalyzer.log
    Cache directory       /var/cache/mutalyzer
    Batchd init script    /etc/init.d/mutalyzer-batchd
    UCSC update crontab   /etc/cron.d/mutalyzer-ucsc-update
    Apache configuration  /etc/apache2/conf.d/mutalyzer.conf
    Static website files  /var/www/mutalyzer/base

The default database user is 'mutalyzer' with no password and the database
names are 'mutalyzer', 'hg18', and 'hg19'.

By default, Mutalyzer is exposed under the '/mutalyzer' url by Apache.

All Mutalyzer processes run under the www-data user and files created and/or
modified by Mutalyzer are owned by this user.

If you have a different environment, or want to customize the default
locations, you can read through these instructions and modify them to your
needs.


Short version
-------------

Run the following commands:

    svn https://www.mutalyzer.nl/svn/mutalyzer2/trunk .
    sudo bash extras/pre-install.sh
    sudo python setup.py install
    sudo bash extras/post-install.sh
    sensible-browser http://localhost/mutalyzer

Or follow the more detailed instructions below.


Automated deployment on a remote host
-------------------------------------

For deploying Mutalyzer on a remote (production or testing) host, we recommend
to automate the steps described below by using Fabric and the included
fabfile. You need Fabric installed on your local machine:

    easy_install fabric

To do a deployment on a server with an existing configured Mutalyzer
installation:

    fab deploy -H server1.mutalyzer.nl

To do a fresh deployment on a new server:

    fab deploy:boostrap=yes -H server1.mutalyzer.nl


Get Mutalyzer
-------------

Since you are reading this, you can probably skip this step. Otherwise, get
your hands on a tarball and:

    tar -zxvf mutalyzer-XXX.tar.gz
    cd mutalyzer-XXX

Or get the source from SVN directly:

    svn https://www.mutalyzer.nl/svn/mutalyzer2/trunk mutalyzer
    cd mutalyzer


Install dependencies
--------------------

If you are on Debian or Ubuntu, you can use the following command to install
all dependencies:

    sudo bash extras/pre-install.sh

Otherwise, install them manually (perhaps have a look in the above script for
a useful dependency list).


Install Mutalyzer
-----------------

Mutalyzer can be installed using Python setuptools. For a production
environment:

    sudo python setup.py install

Alternatively, if you want to have a development environment, use:

    sudo python setup.py develop

The development environment uses symlinks to this source directory, so you can
develop directly from here. This command should be re-issued whenever the
version number of Mutalyzer is updated.


Setup Mutalyzer
---------------

This step creates configuration files and populates the database:

    sudo bash extras/post-install.sh

You can now edit /etc/mutalyzer/config and /etc/apache2/conf.d/mutalyzer.conf
to your likings.


Test the installation
---------------------

You should always test the installation. The tests (for now at least) need
the batch daemon and the webserver (the SOAP part) running.

Now run the tests:

    MUTALYZER_ENV=test nosetests


Upgrade Mutalyzer
-----------------

Unless you installed Mutalyzer in a development environment as described
above, you can upgrade Mutalyzer to a new version by running from the source
directory:

    sudo python setup.py install
    sudo bash extras/post-upgrade

If you installed Mutalyzer in a development environment, you don't have to
do anything to upgrade (apart from updating the source code).


Additional notes
----------------

Included below for future reference is the old install.sh script. It is a bit
outdated.


#!/bin/sh

updateCron() {
  cron_entry="$1 python `pwd`/src/$2.py"

  if ! `crontab -l | grep "$cron_entry" > /dev/null`; then
    echo "Updating cron entry."
    if `crontab -l | grep $2 > /dev/null`; then
      echo "Removing old entry."
      crontab -l | grep -v $2 | crontab
    fi
    echo "Installing new entry."
    (
      crontab -l
      echo $cron_entry
    ) | crontab
  fi
}

if `echo $0 | grep '/' > /dev/null`; then
  echo "Please run this script from the installation directory."
  exit 1
fi

updateCron "25 6 \* \* \*" "UCSC_update"
updateCron "*/1 \* \* \* \*" "BatchChecker"

cat << EOF > .htaccess
SetHandler mod_python
PythonHandler src/handler
PythonPath "sys.path + ['`pwd`/src']"
PythonDebug On

RewriteEngine on
RewriteRule Variant_info.php Variant_info
RewriteRule .*bugtracker.* https://www.mutalyzer.nl/projects/mutalyzer2/
EOF

chmod go+rx . src src/Modules templates
chmod go+r .htaccess mutalyzer.conf src/*.py src/Modules/*.py templates/*
chmod go+rw var