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Linux installation from source (Ubuntu)

Revision as of 10:02, 1 August 2014 by Mark Tsuchida (Talk | contribs)

Note
This page has been updated for the build system changes of r13120, based on testing on Ubuntu 12.04 LTS.

See also: doc/how-to-build.md in the source tree.

Preparation

Install JDK

If you are building the Micro-Manager Java GUI, Java 1.6 or 1.7 is recommended[1]. The simplest way is to use OpenJDK:

Commandline

sudo apt-get install openjdk-6-jdk

(You can also use openjdk-7-jdk.)

Install ImageJ

Download the Linux version of ImageJ from the NIH website. From a terminal, unzip to /usr/local/, and remove the embedded JRE, as we already have one installed.

Commandline

cd ~/Downloads/
sudo unzip ij*-linux*.zip -d /usr/local/
sudo rm -rf /usr/local/ImageJ/jre
sudo chmod a+Xr /usr/local/ImageJ

Install Build Programs and Libraries

You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with:

Commandline

sudo apt-get install subversion build-essential autoconf automake libtool \
                     libboost-all-dev zlib1g-dev swig

You may also need to install additional packages (for cameras and special hardware). See the full list in #Dependencies

Fetch Source Repositories

Create a directory for the the subversion repositories, such as ~/mm. Besides the source tree, additional binary dependencies are stored in the 3rdpartypublic repository. The build scripts in the source tree assume 3rdpartypublic is in the same parent folder level:

Commandline

mkdir ~/mm
cd ~/mm
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
svn co https://valelab.ucsf.edu/svn/3rdpartypublic/

This creates 2 new folders in the mm directory:

    ~/mm/micro-manager1.4
    ~/mm/3rdpartypublic

Building Micro-Manager

Create the Autotools files

Commandline

cd ~/mm/micro-manager1.4
./autogen.sh
./configure --enable-imagej-plugin=/usr/local/ImageJ

Download build dependencies

Commandline

make fetchdeps   # Required since SVN r14001-r14016

Compile

Commandline

make

Install

Commandline

sudo make install

Post Install

Editing the startup script

A script named mmimagej will have been installed in /usr/local/ImageJ. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your PATH.

Running Micro-Manager

Start Micro-Manager by typing:

Commandline

/usr/local/ImageJ/mmimagej 2>&1 >/dev/null &

To view the Core logging in the terminal while Micro-Manager is running, start simply as:

Commandline

/usr/local/ImageJ/mmimagej

Appendix

Dependencies

You need the following packages:
Name Equivalent Synaptic package name
Required Dependencies:
Subversion subversion
GNU C++ build-essential
GNU Autotools autoconf, automake
GNU Libtool libtool
Boost libraries libboost-all-dev
zlib compression library zlib1g-dev
Simplified Wrapper and Interface Library swig
OpenJDK openjdk-6-jdk or openjdk-7-jdk
Optional Dependencies:
Python python-dev, python-numpy-dev
Firewire Camera Library libdc1394-*-dev
Open Source Computer Vision Library libopencv-dev
GPhoto2 libgphoto2-2-dev
FreeImagePlus (used by GPhoto device adapter) libfreeimage-dev
libusb 0.1 libusb-dev
Andor SDK 2/3 N/A - request from Andor website
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