Installation of Reactome database and website

These installation instructions assume that you have root access to the computer onto which you are planning to install Reactome database and website. The instrtuctions are split into two sections, non-Reactome and Reactome. The first of these involves the installation of applications/modules that are not part of the Reactome project but are necessary for the web site to work, such as Apache and MySQL. The second involves installing the Reactome data, modules and web site code.

You do need to have wget, tar, gcc and (gnu) make. Please make sure that those occur in your path and that the "right" one comes 1st.

Non-Reactome software

Perl

Reactome Perl scripts expect the Perl to be at /usr/local/bin/perl. If your Perl installation is otherwise up-to-date but the path to it is different, an easy way to rectify the issue is to create a symbolic link at /usr/local/bin/perl pointing to your Perl executable. E.g. if your Perl is located at /usr/bin/perl, do

ln -s /usr/bin/perl /usr/local/bin/perl

Make sure you have version 5.8.0 or later. If not, install it:

MySQL

The easiest way to install MySQL is to use the pre-compiled binaries from http://dev.mysql.com. Although internally Reactome uses version 4.0, versions 4.1 and 5.0 (the stable release at the time of this writing) do also work. Please note, however, that Perl module DBD::mysql (version 4.001, latest at the tinme of this writing) does not compile against MySQL (mysql-standard-5.0.27-osx10.4-i686 , latest stable release at the time of this writing) on Mac OS X. Please use MySQL 4.1 at least for building DBD::mysql on Macs with Intel processors.

Perl modules

The Reactome website needs quite a few Perl modules to be installed in order for it to run. These modules can all be downloaded from www.cpan.org, and are all installed in much the same way: download the compressed archive, unpack in a working directory, and install the module:

tar xvzf module.tar.gz cd module /usr/local/bin/perl Makefile.PL make make test make install

Please note that some of these modules require installation of further Perl modules. In addition, some of the modules depend on C libraries or executables that have to be installed before the Perl module in question can be installed successfully. Installation of these also follows similar pattern:

tar xvzf package.tar.gz cd package ./configure make make install

Please note that the last step in both of the instructions above requires you to have the root privileges or execute the command as the root user. The latter is achieved by

sudo make install

List of required Perl modules, their purpose and dependencies is as follows. The dependencies are listed in the order in which they have to be installed.

Apache web server

If you don't have Apache web server already, you can download the source code from http://httpd.apache.org/download.cgi. Although Reactome project itself uses version 1.3 of the Apache webserver, later versions (2.2.4 is the most recent one at the time of this writing) do also suffice. For installation instructions please follow the appropriate "Documentation" link on the web page.

Reactome code and data

How to shut down Reactome installation?

How to (re-)start Reactome installation?

You have to execute these commands as the root user.