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, Cluster 3.0 as a command-line program, Pycluster (for Python), and Algorithm::Cluster (for Perl). 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/clustersetup.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 3.0 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 clustersetup.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 installer for Mac OS X, which is 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 Xcode 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 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. Cluster 3.0 as a command line program ------------------------------------- To install the command line version of Cluster 3.0, type ./configure --without-x make make install This will create the executable cluster and install it in /usr/local/bin. Some auxiliary files (such as the documentation) 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). Biopython versions 1.11 and up also contain Pycluster. There, it is referred to as Bio.Cluster. See http://www.biopython.org. 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/. The subdirectory perl/examples contains some example Perl scripts that use Algorithm::Cluster. CONTACT ======= Michiel de Hoon, University of Tokyo, Human Genome Center (currently at the RIKEN Genomic Sciences Center) Email: mdehoon 'AT' gsc.riken.jp