Project: CIPRes 
Version: "Developer 1.0"
Company: San Diego Supercomputer Center

Description:
The CIPRES libraries are designed to enable collaborative efforts in 
  phylogenetic programming.  
The libraries support modules written in Java, C, C++, Perl or Python.
The code in this release is comprised of the libraries themselves (in the 
  framework subdirectory), and  programs that serve as modules
  (in the phyloservices directory) or user-oriented programs (in 
  the cipres-examples subdirectory).

The cipres-examples directory contains a Java application that implements
  the recursive-iterative DCM3 tree searching method of Roshan et 
    
Hardware and software requirements:
  - Requires java version 1.4.2_04 or greater installed on your machine.
  - Use of recidcm3 requires:
    - paup (available at http://paup.csit.fsu.edu/)
    - python version 2.3.  The python that shipped with MacOS X prior to 
        10.4 was slightly broken. To determine if you need to upgrade, 
        see http://www.python.org/download/mac/
  - Building CIPRES requires several third party libraries (omniORB, omniORBpy,
      boost, JacORB, and several perl modules). If you do not have these 
      libraries you can download bundled archives called CIPRES-and-deps.tar.gz
      these archive have all of the third party libraries and are available from
        - http://www.phylo.org/software/maintainer/index.php
      or
        - http://www.phylo.org/software/SDK/index.php
      These bundles contain a python script "configureCIPRES-and-deps.py" 
      which will help you build and install the libraries.

Building:
  The standard steps are:
    - ./configure
    - make
    - make install
  If you are building from the SVN archive (instead from a distributed archive)
    there will not be a configure script.  You can generate it by running
    sh bootstrap.sh
  Use:
    ./configure --help 
    to see the optional arguments to configure.
  The configureCIPRES-and-deps.py script in the CIPRES-and-deps archives 
    (mentioned above) may be helpful even if you have already installed the 
    third party libraries.  It composes a simple shell script with all of the
    command line arguments for configure and enviromental variables.






Troubleshooting:

    Problem: Double-clicking cipres.jar creates a folder called cipres but the 
    application does not launch.

    Solution: This will occur if the default association of .jar files on your 
    machine is with a file compression program and not the java runttime environment. 
    To remedy the situation:

    On Windows: right-click on cipres.jar, select Choose Program, then select javaw 
    from the list of available applications.  Place a check in "Always use the 
    selected program to open this kind of file" to make javaw the default 
    application for .jar files.  Note - if javaw is not among the list of available 
    applications then you need to install java version 1.4.2_04 or greater on 
    your machine ( available at http://java.sun.com/j2se/ )

    On Mac OSX: Under File > Get Info (or cmd+I) Select "Open With.." and then 
    "jar launcher"



TODO Known Problems:
    it is perfect. there are no problems.  it must be your fault. 


TODO: Recidcm3 Performance (times are approximate):

OS          processor          ram        file size(#taxa)    time to do 1 iteration
_______     ________________   ______     ________________    ______________________

Mac OSX     PPC G4 1.5GHz      1Gig       49                   4 sec       
                                          500                  6 sec
                                          7180                 4.5 min

Win XP      Pentium M 1.7GHz   1Gig       49                   4  sec
                                          500                  4  sec
                                          7180                 4.5 min

  
Contact us at:

http://www.phylo.org
TODO: Report bugs at:
http://ngbugz.sdsc.edu/default.php?pg=pgPublicEdit

Date: November 1, 2005