Clustering @ the Coordinated Laboratory for Computational Biology

Special Notes

• UIcluster 3.0 requires mpi to compile. For MPICH, set environment variable CC to mpicc (e.g., setenv CC mpicc). Use mpirun to run a parallel job (e.g., mpirun -np 8 uicluster input_seqs.fasta for an 8 node run).
• If you are submitting the job via PBS, then you need to add the option -machinefile $PBS_NODEFILE to the mpirun command. $PBS_NODEFILE is an environment variable set by the PBS mom. When submitting to the PBS queue, specify the number of nodes in the "resource list" with the -l switch. For example to run on 8 CPU's, you might say #PBS -l nodes=4:ppn=2.
• Running uicluster without any arguments will output useage instructions
• Input data should be masked for repeats and low complexity before clustering

Installation Instructions

1. Unpack distribution: "tar -zxvf uicluster2-1.1.tar.gz"
2. cd uicluster2-1.1
3. ./configure
4. make
5. The executable will be ./uicluster2/uicluster2

Installation Instructions

The cluster viewer is written in Java 1.2 (or 1.1 with Swing 1.1 extensions) and should run properly on Unix, Macintosh, and Windows computers. In order to run the cluster viewer, you need to download and install a Java runtime environment (JRE). Sun has official JRE 1.2 releases for Windows 95/98/NT and Solaris available at http://java.sun.com/products/jdk/1.2/. A pre-release JRE for Linux can be found at http://developer.java.sun.com/developer/earlyAccess/j2sdk122/index.html. Macintosh users will have to use the Apple MRJ 2.1.X which impliments a Java 1.1 JDK. This is available at http://devworld.apple.com/java/text/download.html. In addition, Mac users will need to download the Swing 1.1 libraries from http://java.sun.com/products/jfc/download.html.

The cluster viewer was developed and tested on RedHat Linux 6.0. Instructions are given below for getting it running on both Linux and Windows. Macintosh users are on their own but it should be fairly straight forward the get Java up and running with the instructions that come with the MRJ distribution.

RedHat Linux 6.X

1. Download the Linux JDK1.2 from Sun
2. Detailed installation instructions for Linux are available here. Abbreviated instructions are given below.
3. Extract the JDK distribution in /usr/local/jdk1.2.2
4. Update your path to include /usr/local/jdk1.2.2/bin
5. "which java" should now return "/usr/local/jdk1.2.2/bin/java"
6. Make sure that the environment variables JAVA_HOME and CLASSPATH are NOT set. These are no longer needed with Java 1.2.
7. Download the lastest cluster viewer release here. (shift click)
8. Change directory to the location where uicluster.jar was downloaded. Run it using the following command:
   "java -cp uicluster.jar uicluster.ClusterViewerGUI"

Windows 95/98/NT

1. Download the Windows JDK1.2 from Sun
2. Detailed installation instructions for Windows 95/98/NT are available here
3. Setup the PATH environment variable. The way to do this different for Windows 95/98 and Windows NT. The detailed instructions link above shows how to set the PATH for both systems.
4. From a DOS prompt, type "set". If there is no CLASSPATH entry, then you don't need to do anything. If there is a CLASSPATH entry from a previous Java installation, make sure it includes the current directory '.'. If it doesn't, you won't be able to run java .class files from the current directory.
5. Download the lastest cluster viewer release here. (shift click)
6. Change directory to the location where uicluster.jar was downloaded. Run it using the following command:
   "java -cp uicluster.jar uicluster.ClusterViewerGUI"
   
   NOTE: The above command will only work if you've correctly setup your path to include java.exe and if the CLASSPATH environment variable exists, it includes the current directory '.'

Screenshot

page updated 2/1/2000 by kevin pedretti