CIPRES software source and SDK downloads (external developer's page)

This page will host the CIPRES Software Developers Kit (CIPRES SDK). The SDK contains software and documentation that allow a programmer to integrate their work with CIPRES. Currently the CIPRES libraries are not well documented, and we are not actively soliciting external developers to use the CIPRES library. This page is being used as for developers that are trying out the CIPRES library while consulting with the CIPRES dev team.

If you are a user (and not a developer), you probably are not interested in this page. Pre-release, pre-built versions are available from the snapshot 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).

If you are a maintainer of CIPRES (i.e. you have SVN-write access), you probably want the maintainer page.

We post nightly logs of builds (here) and tests (here).

Prerequisites for all platforms

To build (on any platform) you will need:

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 (Microsoft's Visual Studio .NET 2003 is the tool used for Windows builds. Mac OS and Linux have only been tested on gcc, but should work with other C++ compilers).
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.

On windows it is very helpful to have a "ps" command installed. This is a program that you can run from a command prompt to see a list of all processes you've started and kill them. You might try here from Microsoft .

Installation instructions for Mac and Unix

Building on Mac and Unix-like platforms also requires make. The build procedure (if you are starting from scratch) is:

Download CIPRES-deps-and-source.tar.gz. Make a note of the SVN revision number of the archive from the table here, for use when reporting problems or bugs.
tar xfvz CIPRES-deps-and-source.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-1.0.1/build/share/cipres/resources/cipres.sharedFS.

Try out the installation by running the GUI application CIPRES-and-deps/build/cipres-1.0.1/bin/cipres.sh.

Updating instructions for Mac and Unix

In the future, to obtain newer versions of cipres, you can simply download a new version of CIPRES-deps-and-source.tar.gz, and follow the instructions above to install it (in a different directory). Sometimes this is the simpliest way to go, but you may be able to save time by downloading a new version of the CIPRes software without the dependencies. To update just the CIPRes software:

Run cipresctl stop - to kill the CIPRes registry and property service. The cipresctl program is in CIPRES-and-deps/cipres-1.0.1/build/bin.
Download cipres-1.0.1.tar.gz. Make a note of the the SVN revision number from the table from the table here.
Put the archive in the CIPRES-and-deps directory and expand it by running tar xfvz cipres-1.0.1.tar.gz. (This replaces files in CIPRES-and-deps/cipres-1.0.1.)
Download the configureCIPRES-and-deps.py script, to replace the version in your CIPRES-and-deps directory. Run the script as described in "Installation Instructions for Mac and Unix".

Downloads for Mac and Linux

Archive name	Description	Last updated	SVN revision	Size (MB)
cipres-1.0.1.tar.gz	Just CIPRES code	May, 18, 2009 12:19:36 AM	6488	27.3
CIPRES-deps-and-source.tar.gz	CIPRES and dependencies code	May, 18, 2009 12:19:31 AM	6488	57.8

Make note of the SVN revision number that is associated with your download, and use that number when reporting build problems and bugs. Please note that the version number in the cipres-1.0.1.tar.gz archive name does not reflect a documented and tagged release and doesn't change when the code changes. We will address this soon.

Installation instructions for Windows

Binary distributions of CIPRes are available for Windows on the snapshot page. If you wish to build CIPRes on windows however, you'll need to install all the tools listed here. Note that Microsoft's Visual Studio C++ compiler (v7.1 aka VC2003) is the only supported version. The build procedure if you're starting from scratch is:

Download CIPRES-deps-and-source-win32.zip. Make a note of the SVN revision number from the table here.
jar xvf CIPRES-deps-and-source-win32.zip
cd cipres-and-deps
See cipres-and-deps\readme.txt and set environment variables as it instructs.
From the CIPRES-and-deps directory, run configureTools.bat.

Cipres will be installed in CIPRES-and-deps\cipres-1.0.1\build. Try out the installation by running CIPRES-and-deps\cipres-1.0.1\build\bin\cipres.bat.

Updating instructions for Windows

You only need to download cipres-and-deps-win32.zip and run configureTools.bat once to install the third party libraries. To update just the CIPRes code:

Download cipres-1.0.1.zip. Make a note of the the SVN revision number from the table from the table here.
Put the archive in the CIPRES-and-deps directory and expand it by running jar xvf cipres-1.0.1.zip. (This replaces files in CIPRES-and-deps\cipres-1.0.1.)
From the CIPRES-and-deps directory, run cipres-1.0.1\cipres-build-scripts\build-for-windows\makeCipres.bat.
From the CIPRES-and-deps directory, run cipres-1.0.1\cipres-build-scripts\build-for-windows\installCipres.bat.

Downloads for Windows

Archive name	Description	Last updated	SVN revision	Size (MB)
cipres-1.0.1.zip	Just CIPRES code	Oct, 23, 2008 12:23:34 AM	5702	41.5
CIPRES-deps-and-source.win32.zip	CIPRES and dependencies code	Oct, 23, 2008 12:24:06 AM	5702	84.6

File	Description	Time	Date	Size(MB)
readme.txt	more detailed build instructions (included in CIPRES-deps-and-source-win32.zip)	12:22:30 AM	23-Oct-2008	0
configureTools.bat	script to install tools and get CIPRES from svn (included in CIPRES-deps-and-source-win32.zip)	12:22:41 AM	23-Oct-2008	0