installation for sbmltoolbox failing?

[cbcbc]

Hi everyone,

I'm trying to get SBML running for the COBRA toolbox running and seem to be stuck. On OSX 10.6.8 I have installed SWIG 2.0.4 (--without-pcre) and then

./configure --with-matlab=/Applications/MATLAB_R2012b.app --with-python

And among other things I am getting in the output from this

"

config.status: creating src/bindings/matlab/Makefile

config.status: creating src/bindings/matlab/test/Makefile

(....blah blah blah...)

  Using MATLAB with path        = /Applications/MATLAB_R2012b.app/bin/matlab

"

Which I am taking to mean that the bindings are getting created. But then when I open up matlab and run install.m I get:

"Installing the SBMLToolbox.

* Doing preliminary checks of runtime environment ...

  - This appears to be MATLAB and not Octave.

  - MATLAB reports the OS is 64-bit MacOS.

Checking for libSBML MATLAB binding

libSBML MATLAB binding not found

NOTE: This is not a fatal error.

You will not be able to import or export SBML but can still use the toolbox

to create and manipulate MATLAB_SBML structures

Installation successful

>> "

Can someone tell me what I might be doing wrong, and/or what additional information I need to provide to tell you how to tell me hwat I might be doing wrong? I have also tried with cmake at one point but ended up with the same error when running toolbox's install script. 

Thanks!

[Sarah Keating]

Cross posting to the SBML Software Interoperability Discussion List
<sbml-inter...@googlegroups.com> as this is a better list for
this type of discussion :-)

Hi

Sorry you are having problems.

The install file you need to run is the one that comes with the libSBML
bindings rather than SBMLToolbox.

Within MATLAB navigate to libsbml/src/bindings/matlab.

Here there is a file installSBML which should install the libsbml matlab
bindings. If you run this and then run the SBMLToolbox install file all
should be well.

Alternatively you do not need to build libsbml yourself. We provide
installers for Mac OSX:

https://sourceforge.net/projects/sbml/files/libsbml/5.11.0/stable/Mac%20OS%20X/libsbml-5.11.0-libxml2-macosx-snowleopard.dmg/download

Once installed you need to make sure the folder with the
TranslateSBML/OutputSBML executables and the accompanying matlab scripts
is in the matlab path and then everything should run.

I hope this helps. Let me know if you have further problems.

Sarah