Re: [micro-manager-general] Linux installation

[Jörg H. <joe...@un...>]

Hi Nico,

Thanks, it works (the "script" file in ImageJ is so long, I din't think 
it could be replaced by just 4 lines).

I have summarised my experience for the benefit of other newbies and 
attach installation instructions as an html file to this message. You or 
whoever is managing the website and the packages are welcome to use (and 
correct!) it.

Note that in my case, besides additional hints from this group, the 
instructions in the repository (build_instructions_debian and -unix) had 
to be combined to get the programme working.

Cheers, Jörg

Nico Stuurman wrote:
> 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
>
>   
-- 
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