Hi Marie et al.
When you compile a matlab function like CellProfiler.m, make sure to read the readme.txt file - there really is important info in there! One important feature in readme.txt is to set your path to various libraries, which is what the run_XXX.sh file attempts to set. I believe this is what is causing the above “libxxxx.so.7.6 not found” errors above. You need to know where your MCR is installed, as it is the input argument to the run_CellProfiler.sh command.
See this Mathworks page for more info:
mathworks.com/access/helpdes … g8v-1.html
And yes, you should run CompileWizard on all architectures. Below is the basic CellProfiler compiling procedure (which appears not to have been included in the last few CP Developer’s Version downloads - we are updating and validating this information for the next release).
Directions to compile CellProfiler.m into CellProfiler.exe:
Compilation will destroy your copy of CellProfiler.m - MAKE A COPY and place it somewhere safe.
Open Matlab, cd to the CellProfiler source directory, and run CompileWizard.m by typing in the command line:
cd ~/CellProfiler % change this to wherever your code is
CompileWizard produces two sets of files:
In the Modules directory, each .m file generates a matching .txt file. In the same directory as CellProfiler.m, a new file, CompileWizard_CellProfiler.m, modified for compilation.
Rename CompileWizard_CellProfiler.m to CellProfiler.m (overwriting the old version).
% mv CompileWizard_CellProfiler.m CellProfiler.m
In Matlab, compile CellProfiler:
mcc -m CellProfiler.m -a ‘CPsubfunctions\CPsplash.jpg’
(replace the \ with / on Mac or Linux)
This will produce CellProfiler and CellProfiler.ctf
Create a new directory to hold the compiled version of CellProfiler, with a subdirectory called Modules:
mkdir ~/CompiledCP % change to the desired path
In the shell, change to the CellProfiler source directory, and copy CellProfiler and CellProfiler.ctf to the destination directory (from the first step above), and the .txt files in the Modules directory to the destination’s Modules subdirectory:
cp CellProfiler CellProfiler.ctf ~/CompiledCP
cp Modules/*.txt ~/CompiledCP/Modules
Clean up the source directory:
rm CellProfiler.m Modules/*.txt
restore your copy of CellProfiler.m
Hope this helps,