(If you have no idea what Cartwheel and FamilyRelations are, check out the home page for Cartwheel.)
Logically speaking, there are five major "chunks" of separable code in the Cartwheel/FamilyJewels projects. They are:
People interested in this software will probably also be interested in the Wold Lab Bioinformatics Tools.
At Caltech, we run the public Cartwheel server out of CVS, so there is no real "distribution" per se. You can check out the Cartwheel code from SourceForge like so:
% cvs -d:pserver:email@example.com:/cvsroot/cartwheel login (hit enter at the prompt) % cvs -d:pserver:firstname.lastname@example.org:/cvsroot/cartwheel co cartwheelThe 'woodward' and 'beowulf' tags are the current running versions on our Web site and Beowulf cluster, respectively.
You can get the latest version from SourceForge:
% cvs -d:pserver:email@example.com:/cvsroot/familyjewels login (hit enter at the prompt) % cvs -d:pserver:firstname.lastname@example.org:/cvsroot/familyjewels co FRIIalthough I'd recommend downloading a pre-compiled binary version for Windows or Mac OS X from family.caltech.edu to try it out before grabbing it from CVS.
Some documentation, as well as compilation instructions for Linux, are available under the doc/ directory.
You can get the code by replacing 'co cartwheel' with 'co cartwheel-clients', in the instructions under the Cartwheel server section.
You can get more information on motility here.
You can get paircomp by replacing 'co FRII' with 'co paircomp' in the instructions for getting FRII, above.
Note that under the doc/ directory, there are some notes on the theory behind fixed-width window matching.
However, Caltech's IP office together with my advisor Eric Davidson have been gracious enough to let me release all of the code under either the GPL or LGPL, depending on the package. This means that you are free to take, use, and abuse any and all of the source code for these packages as you will, as long as you extend the same courtesy to everyone else with respect to both the original packages and any modifications you make. Contact me if you have any questions about what this means.
Caltech could well be willing to release parts of this code under a different license; I would be supportive of such an effort, but I'm not interested in pursuing e.g. commercial applications on my own behalf. Let me know if you want me to introduce you to the relevant people in the Caltech IP office.
Cartwheel requires Python 2.3 (or above), as well as recent versions of psycopg, PyXML, and Quixote
Under Windows, I use cygwin to build the binary distribution of FRII, which needs motility, paircomp, and the canal.c++ library from cartwheel-clients (so those all build under cygwin too).
On Mac OS X, everything pretty much just compiles once Xerces and FLTK are installed -- hey, it is UNIX...
Last updated May 2004