Automatically exported from code.google.com/p/consensus-cluster
License
mirekzocalima/consensus-cluster
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
ConsensusCluster PCA and Clustering Utility Copyright Michael Seiler 2008 Rutgers University miseiler@gmail.com ------------------------ Contents: 1. Installation 2. Running ------------------------ 1. INSTALLATION A. Dependencies This program requires the following packages to be correctly installed: Python >= 2.5 Python-numpy >= 1.1.0 In addition, the following optional packages greatly enhance capability: Python-matplotlib >= 0.98.0 (For plots) Python-pil >= 1.1.6 (For consensus matrix heatmaps) Python-pygtk (GUI) Python-scipy (For ttest only, more in the future) psyco (JIT compiler, speed) GCC (Compiler, see Optionally Compile C Extensions below) GNU Make (see Optionally Compile C Extensions below) pyMPI (MPI-compatibility, enables multiprocessor support) Optional dependencies are not required and the program will function without them. This program *MAY* work with versions earlier than those listed, but this has not been tested and such use is unsupported. B. Installation To install, simply untar the package into a new directory. C. Optionally Compile C Extensions (Linux) Optionally, one can compile the external C modules, which are located in the euclidean and SA directories. To compile these, change to the directory, and run make. Example: cd euclidean make && make install Compilation requires python development files, numpy development files, GCC, and GNU make. These extensions are not required, however the program is much slower without them. D. Install precompiled 32-bit C Extensions (Windows) Run the installers in the euclidean and SA directories. These extensions are not required, however the program is much slower without them. 2. RUNNING A. Running ConsensusCluster (Single Processor, Linux and Windows) To run the program, simply type the following from the installation directory: python common.py Or run common.py from any file manager. This will bring up the GUI if pygtk is correctly installed. If not, please see 'python common.py --help' for a complete list of command line options. B. Running ConsensusCluster (MultiProcessor, Linux) If pyMPI is installed and MPI is setup correctly, the following command enables multiprocessor support: mpirun -np 2 pyMPI migration.py Replace "mpirun -np 2" with the appropriate MPI command as required by your MPI installation.
About
Automatically exported from code.google.com/p/consensus-cluster
Resources
License
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published