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How To Build Micro Manager From Source On Ubuntu 13.10

Revision as of 16:51, 22 April 2014 by Mark Tsuchida (Talk | contribs)

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)

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 automake libtool \
libboost1.54-all-dev zlib1g-dev swig \
openjdk-7-jdk python-all-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://rsb.info.nih.gov/ij/download/linux/ij147-linux64.zip
unzip ij147-linux64.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/

# Need to be run two time
./mmUnixBuild.sh ; ./mmUnixBuild.sh

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

# Build binaries (can take a while)
make

# Install MM libs
make install

# Post install stuff
cp bindist/any-platform/MMConfig_demo.cfg $MM_DIR/ImageJ
echo 'macro "AutoRun" {
  run("Micro-Manager Studio");
}' >> $MM_DIR/ImageJ/macros/StartupMacros.txt

# Write start MM script
cd $MM_DIR/ImageJ

# Create mmscript.sh
echo '#!/bin/sh

IJ_PATH=$(pwd)
IJ_LIB=$IJ_PATH/lib/micro-manager
TOOLS_JAR_PATH=$(find /usr -name tools.jar)

export LD_LIBRARY_PATH=.:$IJ_LIB:$LD_LIBRARY_PATH
export CLASSPATH=$IJ_PATH/plugins/Micro-Manager

java -mx4000m \
     -Djava.library.path=$IJ_LIB \
     -Dplugins.dir=$IJ_PATH \
     -cp ij.jar:$TOOLS_JAR_PATH \
     ij.ImageJ
' > mmscript.sh

chmod +x mmscript.sh

# Run MM from ImageJ folder
# ./mmscript.sh
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