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

(Running Micro-Manager: Launch script usage.)
(Dependencies: Update.)
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| GNU C++ || <code>build-essential</code>
 
| GNU C++ || <code>build-essential</code>
 
|-
 
|-
| GNU Autotools || <code>automake</code>
+
| GNU Autotools || <code>autoconf</code>, <code>automake</code>
 
|-
 
|-
 
| GNU Libtool || <code>libtool</code>
 
| GNU Libtool || <code>libtool</code>
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| Simplified Wrapper and Interface Library || <code>swig</code>
 
| Simplified Wrapper and Interface Library || <code>swig</code>
 
|-
 
|-
| Sun Java SDK || N/A - manually fetch from Oracle website
+
| OpenJDK || <code>openjdk-6-jdk</code> or <code>openjdk-7-jdk</code>
 
|-
 
|-
 
|colspan="2"  style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"| Optional Dependencies:
 
|colspan="2"  style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"| Optional Dependencies:
 +
|-
 +
| Python || <code>python-dev</code>, <code>python-numpy-dev</code>
 
|-
 
|-
 
| Firewire Camera Library || <code>libdc1394-*-dev</code>
 
| Firewire Camera Library || <code>libdc1394-*-dev</code>
 
|-
 
|-
 
| Open Source Computer Vision Library || <code>libopencv-dev</code>
 
| Open Source Computer Vision Library || <code>libopencv-dev</code>
 +
|-
 +
| GPhoto2 || <code>libgphoto2-2-dev</code>
 +
|-
 +
| FreeImagePlus (used by GPhoto device adapter) || <code>libfreeimage-dev</code>
 +
|-
 +
| libusb 0.1 || <code>libusb-dev</code>
 
|-
 
|-
 
| Andor SDK 2/3 || N/A - request from Andor website
 
| Andor SDK 2/3 || N/A - request from Andor website

Revision as of 16:43, 22 April 2014

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

Compile

Commandline

make

Install

Commandline

sudo make install-ijplugin
Note
If you have run ./configure without --enable-imagej-plugin, you will be running sudo make install instead. See the build documentation for details.

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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