INSTALLATION
============

The installation procedure depends on the software package you want to use.
Below you will find instructions for Cluster 3.0 for Windows, Mac OS X, and
Unix/Linux, Pycluster (for Python), Algorithm::Cluster (for Perl), and the
C Clustering Library as a stand-alone library.


Cluster 3.0 for Windows
-----------------------

For Cluster 3.0 for Windows, download the Windows installer from our website
(http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ctvsetup.exe). Run
the installer, and you're done.

If for some reason, you want to recompile Cluster 3.0 from the source, you can
use the Makefile in the windows subdirectory. This makefile was used with
Cygwin/Mingw under Windows, and may need to be modified for other systems.
Type
  make
in the windows subdirectory to compile the C Clustering Library, the
Cluster/TreeView GUI, the Windows help files and the documentation. You will
need an ANSI C compiler such as GNU gcc, as well as the GNU windres program to
compile the resources for the GUI. To generate the help files, you will need the
HTML Help SDK, which can be downloaded from Microsoft, as well as the GNU
makeinfo program.
To generate the Windows installer, type
  make ctvsetup.exe
For this, you will need the Inno Setup Compiler, which can be downloaded from
http://www.jrsoftware.org.


Cluster 3.0 for Mac OS X
------------------------

Cluster 3.0 can be installed most easily on Mac OS X by using the prebuilt package, available at http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster.

If you want to recompile Cluster 3.0, it is easiest to use the Project Builder
and Interface Builder that are part of Mac OS X. The subdirectory mac contains
the project file that was used to compile Cluster 3.0.


Cluster 3.0 for Linux/Unix
--------------------------

Cluster 3.0 was ported to Linux/Unix using the Motif libraries. These libraries
are installed on most Linux/Unix computers. You will need a version compliant
with Motif 2.1, such as OpenMotif (http://www.opengroup.org), which is available
at http://www.motifzone.net.

Cluster 3.0 can be installed on Unix/Linux by typing
  ./configure --with-motif
  make
  make install
This will create the executable cluster and install it in /usr/local/bin. Some
auxiliary files are installed in /usr/local/cluster.


Python
------

In the top directory (containing setup.py and also this INSTALL file), type
  python setup.py install
You will need a fairly recent version of Python (2.0 or higher) and the
Numerical Python package, as well as an ANSI C compiler such as GNU gcc. You may
need to log in as root the install Pycluster. If you do not have root access, do
  python setup.py install --prefix=/some/other/directory
and set the environment variable
  PYTHONPATH=/some/other/directory/lib/python2.2/site-packages
The exact command depends on which shell you are using; the exact path will
depend on the version of Python you are using.

Note that Pycluster is also available as a tarball containing only the source
code needed for Pycluster. A Windows installer for Pycluster is available from
our website (http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster).


Perl
----

For Perl, type
  perl Makefile.PL
  make
  make test
  make install
You will need Perl version 5.6 or newer. For the install step, you will need
root access. If you do not have root priviliges, use
  perl Makefile.PL prefix=/some/other/directory
to install the module in /some/other/directory/lib/perl5/.


C Clustering Library
--------------------

To install the C Clustering Library as a static library on Unix-type machines,
in order to call the routines from other C programs, type
  ./configure
  make
  make install
The last step installs the static library libcluster.a and the corresponding
header file cluster.h; you may need to login as superuser for that.

To call the routines from other C programs, #include the cluster.h header file
in your source code, and specify -lcluster when linking.
 

CONTACT
=======

Michiel de Hoon, University of Tokyo, Human Genome Center
mdehoon@ims.u-tokyo.ac.jp


