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
bioperl1.4bio.perl.org
Error0.15CPAN
GD1.41CPAN
Gtk20.95CPAN
IO-String1.01CPAN
libxml0.07CPAN
PodParser1.18CPAN
Usage0.10CPAN
XML-DOM1.42CPAN
XML-Writer0.4CPAN
XML-Twig3.15CPAN

Table 2. Optional Modules for MuGeN

ComponentReleaseAvailable at
SeqDB, Micado and Agmial data retrieval
DBD-Pg1.01CPAN
DBI1.20CPAN
Origami feature data and 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 the usual commands for installing a Perl module:
perl Makefile.PL
make
make install

The executables mugen, mugenb and mugenv are located in a system-wide program directory, like /usr/bin and should be accessible without any specific $PATH settings.

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. If no template file is found when mugen is run for the first time, a default template file will be created.

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 analysis results.