Re: [micro-manager-general] Linux installation

[Nico S. <ni...@cm...>]

Hi Joerg,

> Thanks for the answer, but I'm afraid I'm not sure what to do with it.

Execute it!

> I tried copying the whole or different parts of the above to the
> "script" file in /usr/local/ImageJ (or adding it to "export

I do not know anything about the "script" file in you ImageJ  
directory.  What is important is that LD_LIBRARY_PATH and  
java.library.path are set up correctly when running ImageJ.  The  
script I send (assuming that your ij.jar is in /usr/local/ImageJ) will  
do so.  Save it as run.bsh, and execute it.

> LD_LIBRARY_PATH" therein), but that didn't help. I have to admit  
> that I
> don't understand the java -mx1200m .....ij.ImageJ part at all.

That is the part starting up ImageJ.  It creates a java virtual  
machine and requests 1200 MB of memory.  That line contains some  
parameters that set up the environment for ImageJ correctly.  The  
"script" that you are using must be doing something similar (but it  
looks overly complex).  If you want to modify that script, why not ask  
the authors of your "script" for help?

Best,

Nico



> More
> detailed help would be greatly appreciated! I'm adding part of the
> original "script" file in /usr/local/ImageJ below.
>
> Cheers, Jörg
>
> --------------snip------------------
> # Resolving ij.jar path.  If ij.jar is a symbolic link to  
> ij_<version>.jar
> # this allows updating ij.jar without crashing running sessions
> ij_jar_path=$(derefln ${ij_path}/ij.jar)
>
> for mod_jar in ${ij_path}/lib/*jar  ; do
>    modules="${modules:-}${modules+:}$mod_jar"
> done
> modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
> #${ij_path}/plugins/jars/dcmie.jar
>
> export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
> if (( $verbosity > 0 )) ; then
>    echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
> fi
> -----------snip--------------------------
>
> -- 
> Prof. Jörg Hagmann-Zanolari MD
> University of Basel
> Department of Biomedicine
> Institute of Biochemistry and Genetics
> Mattenstrasse 28
> CH-4058 Basel
> Switzerland
> Phone +41 (0)61 267 3565
>
>
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