Installing MuGeN

System Requirements

MuGeN has been used successfully on Intel/Linux and Sparc/Solaris platforms. It is not intended for use on Windows machines. Disk space requirements are minimal (less than 7 Mb for the programs/modules and documentation, and an additionnal 25 Mb for the example data) but memory footprint can grow as more feature-rich genomes and/or complex analysis results are loaded. For example, the display of two reasonably-sized microbial genomes (about 4 Mb each) and a box plot of the conserved portions between the two of them consumes about 70 Mb of RAM on an Intel/Linux workstation. Line plots having one or more data points per base can be especially memory-consuming.

Software dependencies

MuGeN's programs and modules are all written in Perl. They rely on a set of more or less specialized third-party modules whose list is given in Table 1> (required modules) and Table 2> (optional modules). Notice that these tables only list modules not commonly found in Perl distributions. For a more extensive list of dependencies, see Appendix A>. All of these components are freely available, mostly from CPAN.

Table 1. Modules Needed by MuGeN

ComponentReleaseAvailable at
bioperl1.0bio.perl.org
Error0.15CPAN
GD1.41CPAN
Gtk0.7008CPAN
IO-String1.01CPAN
libxml0.07CPAN
PodParser1.18CPAN
Usage0.10CPAN
XML-DOM1.42CPAN
XML-Writer0.4CPAN

Table 2. Optional Modules for MuGeN

ComponentReleaseAvailable at
SeqDB and Micado data retrieval
DBD-Pg1.01CPAN
DBI1.20CPAN
SeqDB analysis results retrieval
SOAP-Lite0.55CPAN

Installation procedure

MuGeN is available as a gzipped archive. Download the archive in an installation directory and expand its contents by issuing:

gzip -dc mugen-XXXXXXXX.tgz | tar xf -
where XXXXXXXX stands for the release number. This will create a subdirectory called mugen-XXXXXXXX containing all of MuGeN's programs, modules and documentation. cd in this directory and type:
perl install.pl
This will check for the required and optional Perl modules and configure MuGeN's scripts for execution. The absence of one or more optional modules will not prevent the program's installation, only a warning will be issued.

The executables mugen, mugenb and mugenv are located in the MuGeN installation directory. By adding this directory to the $PATH variable the executables can be run from any directory.

MuGeN relies on a preferences file to fix display and database connection parameters. By default, it looks for a file named .mugenrc in the user's $HOME directory. A template preferences file, called mugenrc_template.xml and located in the Data subdirectory can be used for a start and copied to the $HOME directory.

A set of example files, used throughout this document, is available in the mugen-data-XXXXXXXX.tgz archive. This archive can be extracted anywhere and creates a mugen-data-XXXXXXXX directory containing several annotated genomes in GenBank format, as well as some computer anlysis results.