Re: [micro-manager-general] Linux installation

[Jörg H. <joe...@un...>]

Hi Nico,

Thanks for the answer, but I'm afraid I'm not sure what to do with it.
> This means the MMCoreJ_wrap is not in java.library.path. So, you will
> need to add the location of MMCoreJ_wrap.so to your  
> java.library.path.  I once had a "run" script in the repository for  
> that purpose.  I am not sure what replace this on linux, but the  
> startup script looked as follow:
>
> #!/bin/bash
> cd /usr/local/ImageJ
> export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/ 
> local/ImageJ
> java -mx1200m -Djava.library.path=/usr/lib/micro-manager:/usr/local/ 
> ImageJ -Dplugins.dir=/usr/local/ImageJ -cp /usr/local/ImageJ/ij.jar:/ 
> usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ
>   
I tried copying the whole or different parts of the above to the 
"script" file in /usr/local/ImageJ (or adding it to "export 
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. 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