Installing SEEK for other Linux distributions

Our main Install Guide is based upon the Ubuntu 16.04 (LTS) distribution and version. However, other than the distribution packages the install process should be very similar for other distributions.

For some other common distributions, we describe here the required distribution packages, and any other differences we are aware of from our general install guide.

Linux Mint 18

There shoudn’t be any problems once SEEK is installed and running. The only difference we have found is that MySql doesn’t ask for a root password when installing the packages. To initially connect to mysql to setup permissions you may need to do the following:

sudo mysql -u root

Fedora 20 / RHEL / CentOS

This installation was carried out using Fedora 20, but most likely also applies, or is a good starting point, for Red Hat Enterprise Linux, CentOS and other Red Hat based Linux distributions.

Many thanks to Jay Moore for his contributed feedback from his own experiences installing SEEK on RHEL.

Packages

The package names are quite different for Red Hat and are installed using Yum. The packages you need to install are

sudo yum install mysql-server

This actually installed MariaDB, but it is compatible and not a problem. The rest of the packages (included those for running SEEK with Apache) are installed as follows

sudo yum groupinstall "Development Tools" "Development Libraries"
sudo yum install wget curl mercurial ruby openssl-devel  openssh-server git readline-devel
sudo yum install libxml2-devel libxml++-devel java-1.7.0-openjdk-devel sqlite-devel
sudo yum install poppler-utils libreoffice mysql-devel mysql-libs ImageMagick-c++-devel libxslt-devel
sudo yum install libtool gawk libyaml-devel autoconf gdbm-devel ncurses-devel automake bison libffi-devel
sudo yum install httpd-itk httpd-devel

Installing RVM

Install as usual following the INSTALL guide but pay particular attention to any messages it reports about updating your .profile or .bash_profile

Installing Gems

As with Linux Mint and Ubuntu 14.04, you should run the following command before running bundle install to make sure Nokogiri is compiled using the installed version of LibXML

bundle config build.nokogiri --use-system-libraries

Setting up the database

Fedora installs MariaDB instead of Mysql. You may need to start up the database with:

sudo service mariadb start

To make it start at boot-time (this wasn’t enabled by default for me) you should run:

sudo chkconfig mariadb on

To connect to the database to setup the user for SEEK do:

sudo mariadb

Otherwise everything else is the same.

Setting up for production with Passenger Phusion

To start and stop Apache you need to use

sudo apachectl start
sudo apachectl stop

Also, as with MariaDB, it wasn’t set to start at boot-time, so to fix this run:

sudo chkconfig httpd on

The user apache runs under is apache rather than www-data so to create a home directory for that user do:

sudo apachectl stop
sudo usermod -d /home/apache apache
sudo usermod -s /bin/bash apache
sudo mkdir /home/apache
sudo chown apache /home/apache
sudo apachectl start

and instead of using www-data, to switch to that user use:

sudo su - apache

and then proceed with the normal installation, along with the differences to installing the gems and setting up the database described earlier, until you get to install and setup Passenger Phusion.

Before creating the Passenger module, I first need to set the following variable to ensure it was built using a 64bit architecture

export ARCHFLAGS="-arch x86_64"

and then proceed to run

bundle exec passenger-install-apache2-module

I got some warnings about FORTIFY_SOURCE requires compiling with optimization which I ignored and didn’t seem to cause any problems.

At the end compiling and setting up Passenger Phusion, some details about the configuration to apply to Apache are displayed. This should be applied to a config file in /etc/httpd/conf.d/. For e.g. I used a file /etc/httpd/conf.d/seek.conf. You should also remove the other conf files that are put there by default. The contents of this file ended up looking like the following, although yours may differ slightly in terms of the versions used.

LoadModule passenger_module "/home/apache/.rvm/gems/ruby-2.1.2@seek/gems/passenger-4.0.45/buildout/apache2/mod_passenger.so"
<IfModule mod_passenger.c>
   PassengerRoot /home/apache/.rvm/gems/ruby-2.1.2@seek/gems/passenger-4.0.45
   PassengerDefaultRuby /home/apache/.rvm/gems/ruby-2.1.2@seek/wrappers/ruby
</IfModule>

<VirtualHost *:80>
    # !!! Be sure to point DocumentRoot to 'public'!
    DocumentRoot /srv/rails/seek/public
    <Directory /srv/rails/seek/public>
       # This relaxes Apache security settings.
       AllowOverride all
       # MultiViews must be turned off.
       Options -MultiViews
       # Uncomment this if you're on Apache >= 2.4:
       Require all granted
    </Directory>
</VirtualHost>

Afterwards, apache should be restarted with

sudo apachectl restart

Now, I encountered a permission error with loading the module, which I tracked down as being related to SELinux. To get around this I turned off SELinux with

sudo setenforce 0

There is a description of how to be able to re-enable this at http://sergiy.kyrylkov.name/2012/02/26/phusion-passenger-with-apache-on-rhel-6 -centos-6-sl-6-with-selinux but we have been unable to get this to work.

If you have a solution on how to re-enable SELinux, please contact us. You can find details about how to contact us at http://seek4science.org/contact

Ubuntu 10.04 (LTS)

The general packages:

sudo apt-get install wget curl mercurial ruby rdoc ri libopenssl-ruby ruby-dev mysql-server libssl-dev build-essential openssh-server git-core
sudo apt-get install libmysqlclient16-dev libmagick++-dev libxslt-dev libxml++2.6-dev openjdk-6-jdk libsqlite3-dev sqlite3
sudo apt-get install poppler-utils openoffice.org openoffice.org-java-common

To avoid being prompted during the Ruby 1.9.3 installation with RVM:

sudo apt-get install libreadline6-dev libyaml-dev autoconf libgdbm-dev libncurses5-dev automake bison libffi-dev

To install the Passenger Phusion module to run SEEK with Apache:

sudo apt-get install apache2-mpm-prefork apache2-prefork-dev libapr1-dev libaprutil1-dev libcurl4-openssl-dev

The command to start soffice is also slightly different, using just single rather than double hyphens for the arguments:

soffice -headless -accept="socket,host=127.0.0.1,port=8100;urp;" -nofirststartwizard > /dev/null 2>&1 &

If you find the conversion of documents to PDF (for View Content in the browser) is slow, you can install a more recent LibreOffice 3.5 from a separate repository - although this may affect future Operating System upgrades:

sudo apt-get purge openoffice* libreoffice*
sudo apt-get install python-software-properties
sudo add-apt-repository ppa:libreoffice/libreoffice-3-5
sudo apt-get update
sudo apt-get install libreoffice

Debian

By default, the user you create for Debian during the installation is not added to the sudoers list. You may want to add your user to the sudo group e.g

adduser fred sudo

more details can be found at https://wiki.debian.org/sudo

Alternatively, when following the installation run commands that start with sudo as the root user.

The required package names are just the same as for Ubuntu 12.04 - so just follow the install guide.

If you encounter issues related to rvm use - you may need to configure your terminal to run commands as a login shell. There is a checkbox that can be found under the menu Edit, Profile Preferences and then under the tab Title and Command.

Installing SEEK for Mac OS X

Mavericks

This section will guide you to install prerequisite packages, for other steps please read the main Install Guide

You will need first to install Fink and MacPorts, two package manager tools for Mac OS X. Most of the packages will be installed by Finks, while some will be installed by MacPorts Follow this link to install Fink: http://www.finkproject.org/download/index.php?phpLang=en and for MacPorts: https://www.macports.org/install.php

Installing packages

sudo fink install wget curl openssl100-dev git readline6
sudo fink install libxml++2 sqlite3-dev sqlite3
sudo fink install poppler-bin mysql-unified-dev

sudo port install mysql5-server
sudo port install openssh ImageMagick libxslt

For the following packages, you download the dmg image and install manually:

Libreoffice (alternative open office): http://www.libreoffice.org/download
Java JDK: http://www.oracle.com/technetwork/java/javase/downloads/index.html

Other notes

By default, mysql client connects to mysql server through socket at /tmp/mysql.sock. However, you might install by default the .sock file at /opt/local/var/run/mysql56/mysqld.sock. Therefore, the .sock file needs to be re-configured in database.yml

socket: /opt/local/var/run/mysql56/mysqld.sock

And also when you want to run mysql client, you need to give the .sock file path under option -S

You might need to specify the installed location of Libreoffice before running soffice command. E.g. you might add the following line into ~/.bashrc

export PATH="$PATH:/Applications/LibreOffice.app/Contents/MacOS/"