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Difference between revisions of "Linux installation from source (Ubuntu)"

(General remarks (Ubuntu))
(Remove Gentoo instructions, and put them in new Gentoo page)
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== General remarks (Ubuntu)==
+
== General remarks ==
  
 
We assume installation of ImageJ in "/usr/local/ImageJ". If you have installed ImageJ using apt, replace this location with "/usr/share/imagej" wherever it appears below.  In addition to ImageJ and Micro-Manager, you need the following packages:
 
We assume installation of ImageJ in "/usr/local/ImageJ". If you have installed ImageJ using apt, replace this location with "/usr/share/imagej" wherever it appears below.  In addition to ImageJ and Micro-Manager, you need the following packages:
Line 19: Line 19:
 
* Some operations have to be performed as "superuser" ("sudo …").
 
* Some operations have to be performed as "superuser" ("sudo …").
 
* Permissions of the new ImageJ directory might have to be set properly.
 
* Permissions of the new ImageJ directory might have to be set properly.
 
== General remarks (Gentoo) ==
 
 
The ImageJ ebuild can be downloaded from http://bugs.gentoo.org/112275. Digest and install the ebuild (see http://linuxreviews.org/gentoo/ebuilds/).
 
  
 
== Steps ==
 
== Steps ==
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  -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ
 
  -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ
  
== script for Gentoo ==
 
 
Edit '/usr/bin/imagej' according to this:
 
<code><pre>
 
#!/bin/bash
 
 
export LD_LIBRARY_PATH=.:/usr/lib/micro-manager
 
IJ_LIB=/usr/share/imagej/lib
 
 
if !([ "${IJ_HOME}" ]) ; then
 
IJ_HOME=${HOME}
 
fi
 
if [ -d ${IJ_HOME}/plugins ] ; then
 
IJ_PLG=${IJ_HOME}
 
else
 
IJ_PLG=/usr/share/imagej/lib
 
fi
 
if !([ "$IJ_MEM" ]) ; then
 
IJ_MEM=128
 
fi
 
if !([ "$IJ_CP" ]) ; then
 
IJ_CP=$(java-config -p imagej):$(java-config -O)/lib/tools.jar
 
else
 
IJ_CP=$(java-config -p imagej):$(java-config -O)/lib/tools.jar:${IJ_CP}
 
fi
 
$(java-config --java) \
 
-Xmx${IJ_MEM}m -Dswing.aatext=true \
 
-Dawt.useSystemAAFontSettings=on\
 
-cp ${IJ_CP} \
 
-Duser.home=${IJ_HOME} \
 
-Dplugins.dir=${IJ_PLG} \
 
-Djava.library.path=/usr/lib/micro-manager \
 
ij.ImageJ "$@"
 
</pre>
 
</code>
 
  
 
You could run the Micro-Manager in one go by issuing:
 
You could run the Micro-Manager in one go by issuing:

Revision as of 07:44, 23 August 2013

General remarks

We assume installation of ImageJ in "/usr/local/ImageJ". If you have installed ImageJ using apt, replace this location with "/usr/share/imagej" wherever it appears below. In addition to ImageJ and Micro-Manager, you need the following packages:

  • svn for obtaining the repository
  • sun-java6-sdk or better/equivalent
  • autoconf
  • automake
  • swig
  • boost
  • g++
  • libtool
  • libboost 1.2 or newer
  • libdc1394-22-dev

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 https://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. Create a new micro-manager directory in /usr/lib

"sudo mkdir /usr/lib/micro-manager"

5. mmUnixBuild.sh

From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".

6. 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.

7. Run make

"sudo make"

8. Install as superuser

"sudo make install"

9. Run ldconfig

"sudo ldconfig"

10. 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. Make it executable with "sudo chmod +x mmscript".

11. 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 /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


You could run the Micro-Manager in one go by issuing:

 imagej -run "Micro-Manager Studio"
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