Re: installation of libSBML 2.3.4/SBML Toolbox2.0.2
28 Jan '11 09:13
> So far, so good, right?
Congratulations ... at this point you completed installing the Matlab
bindings (or translate SBML) ... if you were to start Matlab in this folder
you could run TranslateSBML('test.xml') and you would get the translated
structure. So this is great for part 1). You might want to make sure the
generated .mexa64 file is in the Matlab path from now on!.
> ===Now, for the SBMLToolbox
> $ PATH="/usr/local/MATLAB/R2010b/bin:$PATH"
> $ echo $PATH
> > /usr/local/MATLAB/R2010b/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:
> > /usr/bin:/sbin:/bin:/usr/games
> $ which mex
> > /usr/local/MATLAB/R2010b/bin/mex
> $ cd /home/celine/Downloads/SBMLToolbox-3.0.0/toolbox
> $ export CFLAGS=-I/usr/local/include
> $ export LDLAGS=-L/usr/local/lib
> ===First try:
> $ make
> > mex -I/usr/local/include -I/usr/local/include -L/usr/local/lib
> > Warning: You are using gcc version "4.4.4-14ubuntu5)". The version
> > currently supported with MEX is "4.3.4".
> > For a list of currently supported compilers see:
> > http://www.mathworks.com/support/compilers/current_release/
> (nothing happens? no warnings, no errors, nothing. only the above)
Stop! ... at this point ... if you closely look at the directory you will
find that you have a shiny new 'OutputSBML.mexa64' in the directory. And
again you are done :) If you add this directory to your Matlab path
(together with the one from above), you can now run:
model = TranslateSBML('test.xml')
And you would find a dialog popping up asking you for the filename where to
safe the file too.
Sorry if this is not as intuitive as it could be ... in the next release we
will be providing scripts with better output. Please let me know if you
continue to have trouble