Re: [micro-manager-general] Linux installation
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Re: [micro-manager-general] Linux installation
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From: Jörg H. <joe...@un...> - 2009-07-09 14:56:15
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Sorry, forgot an essential step not found in the official documents:
creating /usr/lib/micro-manager (step 4 in the new instructions). Please
replace with the new attachment.
Cheers, Jörg
Jörg Hagmann wrote:
> 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
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> Installation on a Linux system
>>
>>
>> Table of Contents
>>
>> * Installing Micro-Manager from source <#sec-1>
>> o General remarks <#sec-1.1>
>> o Steps <#sec-1.2>
>> o mmscript: <#sec-1.3>
>>
>>
>> Installing Micro-Manager from source
>>
>>
>> General remarks
>>
>> We assume installation of ImageJ in "/usr/local/ImageJ". In addition
>> to ImageJ and Micro-Manager, you need the following programmes:
>>
>> * svn for obtaining the repository
>> * sun-java6-sdk or better/equivalent
>> * autoconf
>> * automake
>> * swig
>> * libace
>> * libace-dev
>> * g++
>> * libtool
>>
>> In addition, note that:
>>
>> * File versions might have changed, check before using the names
>> given in the instructions.
>> * Some operations have to be performed as "superuser" ("sudo …").
>> * Permissions of the new ImageJ directory might have to be set
>> properly.
>>
>>
>> Steps
>>
>> 1. *Installing ImageJ*
>> Get the Linux version of ImageJ from
>> http://rsb.info.nih.gov/ij/download.html, move it to
>> "/usr/local" and unpack it as described in
>> http://rsb.info.nih.gov/ij/docs/install/linux.html. You will
>> have a directory "/usr/local/ImageJ" with everything needed to
>> run ImageJ (you can start ImageJ from the terminal: "cd
>> /usr/local/ImageJ", followed by "./run").
>> 2. *Get Micro-Manager from the repository*
>> Make a directory somewhere (e.g. "~/src"), move to it ("cd
>> ~/src") and get Micro-Manager with the command "svn checkout
>> htpps://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3".
>> This will download all the necessary files from the repository
>> into "~/src/micromanager1.3/".
>> 3. *Beanshell and swingx*
>> Move to the new directory ("cd micromanager1.3") and copy
>> beanshell and swingx from "~/src/micromanager1.3/classext" to
>> the "plugins" directory of your ImageJ installation: "sudo cp
>> classext/bsh-2.0b4.jar /usr/local/ImageJ/plugins" and "sudo cp
>> classext/swingx-0.9.5.jar /usr/local/ImageJ/plugins".
>> 4. *mmUnixBuild.sh*
>> >From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".
>> 5. *Run configure*
>> "./configure --with-imagej=/usr/local/ImageJ". You have to add
>> the option (--with-imagej), because the default assumes a
>> different localisation of ImageJ.
>> 6. *Run make*
>> "make"
>> 7. *Install as superuser*
>> "sudo make install"
>> 8. *Run ldconfig*
>> "ldconfig"
>> 9. *The starting script*
>> Starting ImageJ with the scripts provided in the ImageJ
>> directory (run, script, see 1 above) will start ImageJ, but
>> Micro-Manager, although now in the plugins directory, will not
>> work properly because the path to /usr/lib/micro-manager is
>> missing. Write your own script containing the 4 lines given
>> below ("mmscript"), save and move it to /usr/local/ImageJ.
>> 10. *Running Micro-Manager* cd to "/usr/local/ImageJ" and start
>> ImageJ with your new script ("./mmscript &"). In the plugins
>> menu of ImageJ, start Micro-Manager –> Micro-Manager Studio.
>>
>>
>> mmscript:
>>
>> ------------------------------------------------------------------------
>> #!/bin/bash
>> cd /user/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
>>
>> ------------------------------------------------------------------------
>> ------------------------------------------------------------------------
>>
>> Author: Jörg Hagmann <joerg.hagmann at unibas.ch>
>> <mailto:joerg.hagmann%20at%20unibas.ch>
>>
>> Date: 2009-07-09 15:35:16 CEST
>>
>> HTML generated by org-mode 6.28trans in emacs 22
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
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>>
--
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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