T Coffee Install From Distribution

How compile and install T-Coffee from source distribution package

T-Coffee installation from source distribution package

Introduction

If you need a custom installation of T-Coffee, you can compile and install it using the source distribution. T-Coffee can be compiled on Unix/Linux and Mac OSX platform. Microsoft Windows operating system is supported via Cygwin compatibility layer.

Prerequisites

T-Coffee compilation requires the following tools installed on your system gcc, g77, make, CPAN. Moreover you will need an internet connection and the root account password.

UNIX/LINUX/Mac OSX

Download from the following path [the source distribution package named T-COFFEE_distribution_<version>.tar.gz .

Open a shell window, move in the folder you have downloaded the distribution package and type the following command:

1. tar -xvf T-COFFEE_distribution_<version>.tar
2. cd T-COFFEE_distribution_<version>
3. ./install all

This installation procedure is semi-interactive. It will prompt questions here and there. You can interrupt it any time and resume it later.

The install procedure carries out three distinct tasks:

1. Compilation of T-Coffee (C program).
2. Compilation and Installation of SOAP::Lite and XML::Simple (Perl modules).
3. Download/Compilation and Installation of all the T-Coffee companion packages required for all possible T-Coffee flavors (tcoffee, expresso, mcoffee, rcoffee, etc).

The compiled binaries will be installed in the following path ~/.t_coffee/plugins/<osname> (where osname represent your platform name) . Make sure these executables are on your $PATH !).

Except for T-Coffee, the installer will only install the packages that are NOT already on your computer. If you want a lighter or more specific installation, you can try any of the following:

• ./install tcoffee
• ./install rcoffee
• ./install expresso
• ./install mcoffee

While Installing SOAP::Lite, CPAN will ask you many questions: say Yes to all or type return to keep the default values.

If you cannot log as root, or if for some reason this procedure does not work, see with your system manager and/or go directly to the CPAN repository of SOAP::Lite. You will still be able to use the most basic functions of T-Coffee.

IMPORTANT: The purpose of SOAP::Lite is to allow T-Coffee the use of the EBI webservices such as webblast. BLAST brings many functionalities to T-Coffee and if you cannot install SOAP we suggest you go to the Installing BLAST for T-Coffee section of the Technical Doumentation (in the Installation section). There you will find alternative ways of using BLAST without SOAP. It is also in this document that you will find all the information required for a full installation of T-Coffee.

Microsoft Windows/Cygwin

Support with Microsoft Windows platform relies on http://www.cygwin.com/ Cygwin. Follow the following steps to install T-Coffee on Windows:

1. Download The Installer (NOT Cygwin/X)
2. Click on view to list ALL the packages
3. Select: gcc-core, make, wget
4. Optional: ssh, xemacs, nano
5. Run mkpasswd in Cywin (as requested when you start cygwin)

Finally install T-Coffee within Cygwin using the Unix procedure. This installation procedure is really tricky and has not been tested with the latests version.

A much more handy alternative consists to install a Linux guest on your Windows workstation using a common virtualization tool (like VMware, VirtualBox, etc) and install T-Coffee in the virtualized machine following the Unix procedure.