Mussa: Multi-species sequence analysis

You might think of it as an acronym, but its pretty much become a proper name in my mind.  So no going around writing MUSSA or even M.U.S.S.A - this isn't a secret gov't military program or 70s era mainframe (which is what all those caps put me in the mind of).

There isn't much to this README yet.  Basic info on compiling and using mussa is available on the website at http://mussa.caltech.edu

I will get around to a more informative README eventually.


The main problem you will likely encounter trying to compile Mussa is with the fltk libraries.  If you try to compile mussa and you get errors like the following, either you do not have the fltk libraries installed or they are located someplace gcc is not looking.  If you know fltk libraries are on the system, you need to try messing with the various LDFLAGS examples in the Makefile.

"""
g++ -ftemplate-depth-25 -c mussa_gui_seq.cc
In file included from mussa_gui_annot_window.hh:1,
                 from mussa_gui_load_window.hh:1,
                 from mussa_gui_seq_view.hh:1,
                 from mussa_gui_seq.hh:1,
                 from mussa_gui_seq.cc:1:
mussa_gui_motif_window.hh:3:19: error: FL/Fl.H: No such file or directory
mussa_gui_motif_window.hh:4:26: error: FL/Fl_Window.H: No such file or directory
mussa_gui_motif_window.hh:5:26: error: FL/Fl_Button.H: No such file or directory
mussa_gui_motif_window.hh:7:25: error: FL/Fl_Input.H: No such file or directory
mussa_gui_motif_window.hh:8:26: error: FL/Fl_Output.H: No such file or directory
mussa_gui_motif_window.hh:9:24: error: FL/Fl_Pack.H: No such file or directory
"""

If you have other issues, or find bugs, email me: tristan@caltech.edu - preferably indicating its about Mussa in the subject :)

There are some known bugs/incomplete features documented in the tutorial info on the website.

If you want to compile this under OSX for use on the command line, just use the appropriate set of marked LDFLAGS in the Makefile.  However, there are a number of oddities, of which I will just cover a few.  Use from the command line will work just like a unix/linux system, but gui windows will not come into the forground.  If you try to put the Mussa executable into a .app folder like the pre-compiled version offered at mussa.caltech.edu, the system sends odd command line args which confuse my poor program.  There are things which need to be commented out in the code.  Some of these are marked, others not.  Why not just use the precompiled version and drink a beer later with the time you saved?


Tristan  De Buysscher