SCaFoS
Selection, Concatenation and Fusion of Sequences

Technical requirements

The current version runs on Linux, Windows XP and Mac OS X. Potentially SCaFoS could run on all Unix-like operating systems (Debian, Fedora, Gentoo, Mandrake, RedHat, Slackware, SuSE, ...), but the software has only been tested on Red-Hat and Fedora and is provided as is.
SCaFoS requires Perl version 5.8.0 or later, Tk version 8.4.5 or later and Tree-puzzle version 5.1 or later. You can download the latest version from their respective web site:

Installation on Linux

required tools

On most linux systems, Perl will be probably already installed and you only have to verify the version with the following command:

perl -v

You can also verify the Tk installation by typing the command:

perl -e 'use Tk'

If Tk is not installed, an error message is displayed.
Before installing Tk, be sure to have the X11 development library on your system.

To install these modules it's better to have administrator permissions. The purpose of this part is not to explain in detail how to install these pre-required softwares, but only to guidelines to typical user. For more information, please, refer to the online sites of the products that take into account the specificities of the various operating systems.

3 major ways are available to install packages on linux:
  • from the sourcefile, the different usual steps to install a package located in the current directory are (in all cases, read the README file which includes installation specificities):
    • to uncompress and unpack the sourcefile:
gzip -d SourceFile.tar.gz
tar -xvf SourceFile.tar
    • to built the package from the newly created directory:
cd 'NewDirectory'
./configure
perl MakeFile.PL
make
    • to install the package:
make install
  • from a RedHat Package Manager file (RPM) :
    • for a new installation:
rpm -ivh PackageFile.rpm
    • for updating a package:
rpm -Uvh PackageFile.rpm
  • from the Comprehensive Perl Archive Network (CPAN),you need to be connected as root and to have access to internet; you have to type the following commands and answer to the questions (a lot are predefined and you have just to type ENTER) :
perl -MCPAN -e'install Perl'
perl -MCPAN -e'install Tk'

If errors appear during test steps of the Tk Installation, you can force the installation by the following command in a CPAN session:

force install Tk

As SCaFoS has to be independent of the TREE-PUZZLE version, it is necessary to rename the executable file with the standard name puzzle:

mv tree-puzzle puzzle


SCaFoS

Create a SCaFoS directory and change to this directory:

mkdir scafos
cd scafos

To install the Perl script, copy the source file in the SCaFoS directory and uncompress it by typing the following commands (xxx means the version number):

gzip -d scafos_scr_linux.xxx.tgz tar -xvf scafos_src_linux.xxx.tar

To be able to run SCaFoS from all directories, it is necesary to add a new environment variable in your system.
To simplify software loading, an executable file (not compiled) is provided: its file name is scafos
You must add the following line in the file .bash_profile or type it before each running session of SCaFoS:

export SCAFOS=$HOME/scafos
let scafos be the directory name where SCaFoS is installed

To enable the environment variable, you must close your session or use the source UNIX command to force the shell to read the .bash_profile file:

source .bash_profile


Installation on Windows XP

SCaFoS installation needs permission to create directories and system variables.

required tools

To install the pre-required tools under Windows, the easy way is to use the MSI installer with the files provided by the ActiveState web site and to follow the explanations.

SCaFoS

To install SCaFoS, create a SCaFoS directory, copy the source file in this directory and uncompres it: a right click on the scafos_src_linux.xxx.zip file opens a menu where you chose the Extract All function. You could also use your favorite uncompress tool like Winzip or an other one.

The easiest way to create the environment variable under Windows:
  • click on the Start menu,
  • point to My Computer,
  • open a new menu by a right click,
  • click on Properties,
  • in the new opened window choose the Advanced tab
  • click on Environment Variables button, select New in the user variables,
  • in the new window, type SCAFOS in the Variable name zone and the full path of the directory where SCaFoS is installed in the Variable value zone
  • close all windows by click on the OK buttons


Installation on Mac OS X
Mac OS X is compatible with UNIX systems. So to run SCaFoS, not only Perl must be installed, but also X11 program and Perl-tk. The following procedure has been tested for Intel-based Macs, but it should work for PowerPC-based Macs also. For more detailed information, refer to the Apple web site.

required tools

Generaly, Perl is preinstalled on your system: you can test it in a terminal window by the following command that displays the perl version if installed:

perl -v

As UNIX application, ScaFoS runs in a terminal window and some installation steps require this type of window also. You access the UNIX operating system in Mac OS X by using the terminal application. Terminal is in the Applications > Utilities folder.

If you did not install X11 during Mac OS X installation:
  • insert the Mac OS X Install disc,
  • double-click the Optional Installs package,
  • follow the on-screen instructions until you see a list of software packages,
  • open Applications,
  • select X11
To install Perl-tk, you need to be a superuser (you may need to type an administrator password to make these changes):
  • open NetInfo Manager, located in Applications > Utilities.
  • in the top menu, choose Security > Enable Root User
  • type a password for the root account.
  • in a terminal window, type su and the password root
  • type the following command to launch the Perl-tk installation :
perl -MCPAN -e'install Tk'

  • exit from the root session

SCaFoS

All steps of the SCaFoS installation are made in a terminal window. Create a SCaFoS directory and change to it:

mkdir scafos
cd scafos

To install the Perl script, copy the source file in the SCaFoS directory and uncompress it by typing the following commands (xxx means the version number):

gzip -d scafos_scr_linux.xxx.tgz
tar -xvf scafos_src_linux.xxx.tar

Copy and uncompress the source file in this directory. To enable the SCaFoS script, you must add the following line in the   .profile file (if the file does not exist, create it in your Home directory):

export SCAFOS=$HOME/scafos
let scafos be the directory name where SCaFoS is installed

To enable the environment variable, you must close the terminal window or use the source UNIX command to force the shell to read the .profile file:

source .profile

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