CIPRES software maintainer downloads

This page hosts archives of CIPRES software intended for maintainers of CIPRES -- folks with SVN access.

Note: read-only access to the svn repository is publicly available -- instructions are here). External developers who are interested in using CIPRES, but prefer a downloadable archive of the soure code (rather than using svn) should see the external developers page.

More information about the CIPRES software development can be found at:

The CIPRES overview page.
The CIPRES Developers TWiki (see this page for information about access to the Wiki).

Prerequisites in for all platforms

All maintainers will need:

Subversion (SVN) (available here).
Apache ant version 1.6.5 (available here).
Python version 2.4 (available here).
Java SDK version 1.5 (available here, look under "Previous Releases" for version 1.5. Later versions may work, but haven't been tested.)
Perl is required to have access to some modules (the recommended download is from Active State here).
A C++ compiler is required for some modules (Microsoft's Visual Studio is the tool used for Windows builds. Only gcc has been tested on Mac and Linux.)
PAUP Version 4 (available here) is required to run CIPRes; in the future, it won't be mandatory.

Set your PATH environment variable such that ant, python, javac, java, paup (and perl, if using) can be run from the command line.

Downloads and instructions for Mac and Unix

Maintainers building on Mac and Unix-like platforms will need:

Automake version 1.9 or greater (available here).
Autoconf
make

The build procedure (if you are starting from scratch) is:

Download CIPRES-deps.tar.gz
tar xfvz CIPRES-deps.tar.gz
cd CIPRES-and-deps
python configureCIPRES-and-deps.py -p < /dev/null

configureCIPRES-and-deps.py installs the third party libraries that are used by CIPRes and creates a shell script that invokes configure with the correct arguments. The -p option to configureCIPRES-and-deps.py tells it not to install the perl parts of CIPRes (by adding the --disable-perl-lib flag to the configure command). The perl modules add quite a bit of time to the initial configuration and CIPRes is usable without the perl components so you may want to start without them. On the other hand, if you plan to use the perl parts of CIPRes or develop perl modules for CIPRes, omit the -p argument (or rerun the command later without the -p).

If you're installing CIPRes to a shared filesystem and will run CIPRes from multiple hosts you must also: touch CIPRES-and-deps/cipres/build/share/cipres/resources/cipres.sharedFS.

Try out the installation by running the GUI application CIPRES-and-deps/build/cipres/bin/cipres.sh.

File	Description	Time	Date	Size(MB)
CIPRES-deps.tar.gz	Boost, omniORB, JacORB, perl modules, and script for getting CIPRES using svn	12:18:21 AM	05-Jul-2008	29.3
configureCIPRES-and-deps.py	interactive script that helps you compose the correct arguments to the CIPRES configure script	12:18:30 AM	05-Jul-2008	0.0418

Downloads and instructions for Windows

Maintainers building on Windows XP will need to install the tools described above in "Prerequisites for All Platforms". The only compiler that's currently supported is Microsoft Visual Studio .NET 2003 (aka VC 7.1).

The build procedure if you're starting from scratch is:

Download CIPRES-deps-win32.zip
jar xvf CIPRES-deps-win32.zip
cd cipres-and-deps
See cipres-and-deps\readme.txt and set environment variables as it instructs.
configureTools.bat

Cipres will be installed in cipres-and-deps\cipres\build. Try out the installation by running cipres-and-deps\build\bin\cipres.bat.

You only need to download CIPRES-deps-win32.zip and run configureTools.bat once to install the third party libraries. After that you can checkout the latest version of cipres from subversion into cipres-and-deps\cipres, and rebuild by:

cd CIPRES-and-deps
cipres\cipres-build-scripts\build-for-windows\makeCipres.bat
cipres\cipres-build-scripts\build-for-windows\installCipres.bat

File	Description	Time	Date	Size(MB)
CIPRES-deps-win32.zip	Boost, omniORB, JacORB, and script to install them and get CIPRES using svn	06:46:30 AM	04-Jul-2008	42.9
readme.txt	more detailed build instructions (included in CIPRES-deps-win32.zip)	06:46:41 AM	04-Jul-2008	0.0042
configureTools.bat	script to install tools and get CIPRES from svn (included in CIPRES-deps-win32.zip)	06:46:52 AM	04-Jul-2008	0.0046

For Java Developers: Using Eclipse

On the Mac and Linux, the CIPRes software uses an autoconf-based configure script to unify all of the build-time decisions in one place. The system uses autoconf and automake to generate a configure script and Makefiles. All (non-Windows) maintainers must use the Makefiles and run "make install" at least once. After the skeleton of a CIPRES installation is created, Eclipse may be used for your daily work on the java parts of the library.

You will have to rerun configure if the location of required libraries changes, and you will have to rerun "make install" if any of the code in cipres/framework/IDL changes, or if you need to pick up changes that other CIPRes maintainers have made to the C++, python or perl code. When adding, removing, or moving files and directories, please remember to update the build.xml and Makefile.am files as needed. Remember that other developers will be using the configure/make/make install process, not Eclipse, to build CIPRes.

The same information applies to Windows, except that configureTools.bat, makeCipres.bat and installCipres.bat are the core of the canonical build system (instead of autoconf/automate/configure).

There is an Eclipse .project file in CIPRES-and-deps/cipres to get you started.

Third Party Libraries

The following third party libraries are required to build cipres and are included in CIPRES-and-deps.tgz and CIPRES-deps-win32.zip and installed by the scripts described above. More information is available from these links:

JacORB version 2.2.2 or greater (available here).
omniORB version 4.0.6 or greater (homepage here; the recommended version is 4.0.7. The prebuilt windows version is omniORB-4.0.7-win32-vc7.zip).
omniORBpy. Its important to have the version that "goes" with the version of omniORB that you have (homepage here; the recommended version is 2.7. The prebuilt windows version is omniORBpy-2.7-win32-python2.4.zip).
The Boost C++ libraries (available here).