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Difference between revisions of "How To Build Micro Manager From Source On Ubuntu 13.10"

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{{Note|This page has not yet been updated to reflect the build system changes of r13120. Some of the steps below are no longer necessary, or need slight modification. See also: [[Linux installation from source (Ubuntu)]]}}
+
{{Note|This page has been updated to reflect the build system changes of r13120, but the updated script has not been tested. Ask on the mailing list if you run into issues.}}
  
 
Here is a small script I use to build MM on Linux to be able to test new features and develop plugins with DemoAdaptaters. I can provide help to adapt build system to your Linux. Contact me on the MM mailing list: https://micro-manager.org/wiki/Micro-Manager_Community.
 
Here is a small script I use to build MM on Linux to be able to test new features and develop plugins with DemoAdaptaters. I can provide help to adapt build system to your Linux. Contact me on the MM mailing list: https://micro-manager.org/wiki/Micro-Manager_Community.
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# Instal dependencies
 
# Instal dependencies
Here you have debian packages you can install with sudo apt-get install
+
# Here you have debian packages you can install with sudo apt-get install
Find equivalent packages for others distributions:
+
# Find equivalent packages for others distributions:
subversion build-essential automake libtool \
+
#
libboost1.54-all-dev zlib1g-dev swig \
+
# subversion build-essential autoconf automake libtool \
openjdk-7-jdk python-all-dev
+
# libboost1.54-all-dev zlib1g-dev swig \
 +
# openjdk-7-jdk python-dev python-numpy-dev
  
 
mkdir mm/
 
mkdir mm/
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# Get ImageJ (use it even if you already have another copy of ImageJ or Fiji)
 
# Get ImageJ (use it even if you already have another copy of ImageJ or Fiji)
wget http://rsb.info.nih.gov/ij/download/linux/ij147-linux64.zip
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wget http://imagej.nih.gov/ij/download/zips/ij148.zip
unzip ij147-linux64.zip
+
unzip ij148.zip
  
 
# Retrieve MM source code (can be long)
 
# Retrieve MM source code (can be long)
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cd micro-manager/
 
cd micro-manager/
  
# Need to be run two time
+
./autogen.sh
./mmUnixBuild.sh ; ./mmUnixBuild.sh
+
  
./configure --prefix=$MM_DIR/ImageJ --with-imagej=$MM_DIR/ImageJ --enable-python
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./configure --prefix=$MM_DIR/ImageJ --enable-imagej-plugin=$MM_DIR/ImageJ --with-python
  
 
# Build binaries (can take a while)
 
# Build binaries (can take a while)
 
make
 
make
  
# Install MM libs
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# Install MM as ImageJ plugin
make install
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make install-ijplugin
  
# Post install stuff
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# Run MM
cp bindist/any-platform/MMConfig_demo.cfg $MM_DIR/ImageJ
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# $MM_DIR/mmimagej
echo 'macro "AutoRun" {
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  run("Micro-Manager Studio");
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}' >> $MM_DIR/ImageJ/macros/StartupMacros.txt
+
 
+
# Write start MM script
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cd $MM_DIR/ImageJ
+
 
+
# Create mmscript.sh
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echo '#!/bin/sh
+
 
+
IJ_PATH=$(pwd)
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IJ_LIB=$IJ_PATH/lib/micro-manager
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TOOLS_JAR_PATH=$(find /usr -name tools.jar)
+
 
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export LD_LIBRARY_PATH=.:$IJ_LIB:$LD_LIBRARY_PATH
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export CLASSPATH=$IJ_PATH/plugins/Micro-Manager
+
 
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java -mx4000m \
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    -Djava.library.path=$IJ_LIB \
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    -Dplugins.dir=$IJ_PATH \
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    -cp ij.jar:$TOOLS_JAR_PATH \
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    ij.ImageJ
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' > mmscript.sh
+
 
+
chmod +x mmscript.sh
+
 
+
# Run MM from ImageJ folder
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# ./mmscript.sh
+
 
</pre>}}
 
</pre>}}

Revision as of 17:02, 22 April 2014

Note
This page has been updated to reflect the build system changes of r13120, but the updated script has not been tested. Ask on the mailing list if you run into issues.

Here is a small script I use to build MM on Linux to be able to test new features and develop plugins with DemoAdaptaters. I can provide help to adapt build system to your Linux. Contact me on the MM mailing list: https://micro-manager.org/wiki/Micro-Manager_Community.

Command Line

# Instal dependencies
# Here you have debian packages you can install with sudo apt-get install
# Find equivalent packages for others distributions:
#
# subversion build-essential autoconf automake libtool \
# libboost1.54-all-dev zlib1g-dev swig \
# openjdk-7-jdk python-dev python-numpy-dev

mkdir mm/
cd mm/

# Save directory path
MM_DIR=$(pwd)

# Get ImageJ (use it even if you already have another copy of ImageJ or Fiji)
wget http://imagej.nih.gov/ij/download/zips/ij148.zip
unzip ij148.zip

# Retrieve MM source code (can be long)
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk micro-manager
svn co https://valelab.ucsf.edu/svn/3rdpartypublic

# Build MM
cd micro-manager/

./autogen.sh

./configure --prefix=$MM_DIR/ImageJ --enable-imagej-plugin=$MM_DIR/ImageJ --with-python

# Build binaries (can take a while)
make

# Install MM as ImageJ plugin
make install-ijplugin

# Run MM
# $MM_DIR/mmimagej
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