This page has been updated to reflect the build system changes of r13120 and r13223, 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.
# 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 pkg-config \
# libboost1.54-all-dev zlib1g-dev swig \
# openjdk-7-jdk ant 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
# Download build dependencies
make fetchdeps # Required since SVN r14001-r14016
# Build binaries (can take a while)
make
# Install MM as ImageJ plugin
make install
# Run MM
# $MM_DIR/mmimagej