The Cartwheel Bioinformatics Toolkit
All of the Cartwheel and FamilyJewels source stuff has been moved from the two SourceForge sites (http://sf.net/projects/cartwheel and http://sf.net/projects/familyjewels/) into a single Subversion repository. All of the "active" projects are now available under /trunk/, e.g. /trunk/FRII contains the active development code for FamilyRelationsII.
You can check out individual modules like this:
svn co http://svn.idyll.org/repos/cartwheel/trunk/FRII FRII
Developers can use ssh:
svn co svn+ssh://<user>@svn.idyll.org/svn/t/cartwheel/trunk/FRII FRII
You're probably interested in one or more of the following modules: FRII, cartwheel-server, motility, or paircomp.
Contact Titus Brown at email@example.com if you need check-in access or you would like an account to submit tickets, edit documentation on this Wiki, etc.
Announcements of new features and new releases will be made to the cartwheel-announce list.
The cartwheel list is the place for discussion.
If you are interested in ongoing development, the Cartwheel subversion announcements list reports all check-ins. (Subscribe to this if you're actively interested in the Cartwheel source code!)
There is documentation for most of the individual packages under the doc/ subdirectories, e.g. FRII/doc or cartwheel-server/doc.
Building the Software
Here's a page on BuildingFamilyRelations. If you want to build paircomp or motility independently, just run cmake . && make in the paircomp/ or motility/ subdirectory.
Developers with check-in privileges might check the Cartwheel buildbot page.