Difference between revisions of "Linux installation from source (Ubuntu)"
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== Preparation == | == Preparation == | ||
| − | === | + | === Install ImageJ === |
| − | {{ | + | [http://rsb.info.nih.gov/ij/download.html Download the Linux version of ImageJ] from the NIH website and follow the installation instructions there. Test that ImageJ runs from a terminal: |
| − | + | ||
| + | {{MessageBox|1=Commandline|2=<pre> | ||
| + | |||
| + | cd /usr/local/ImageJ/ | ||
| + | ./run | ||
| + | </pre>}} | ||
| + | |||
| + | === Other Required Programs and Libraries === | ||
You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with: | You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with: | ||
| Line 15: | Line 22: | ||
</pre>}} | </pre>}} | ||
| − | You may also need to install additional | + | You may also need to install additional packages (for cameras and special hardware). See the full list in [[#Dependencies]] |
=== Source Repositories === | === Source Repositories === | ||
| Line 31: | Line 38: | ||
This creates 2 new folders in the <code>mm</code> directory: | This creates 2 new folders in the <code>mm</code> directory: | ||
<pre> | <pre> | ||
| − | ~/mm/micro-manager1.4 | + | ~/mm/micro-manager1.4 |
| − | ~/mm/3rdpartypublic | + | ~/mm/3rdpartypublic |
</pre> | </pre> | ||
| Line 40: | Line 47: | ||
cd ~/mm/3rdpartypublic/classext | cd ~/mm/3rdpartypublic/classext | ||
| − | sudo cp bsh-2.0b4.jar swingx-0.9.5.jar /usr/local/ImageJ/plugins | + | sudo cp bsh-2.0b4.jar swingx-0.9.5.jar /usr/local/ImageJ/plugins/ |
</pre>}} | </pre>}} | ||
| − | Create a new micro-manager directory in /usr/lib | + | Create a new micro-manager directory in /usr/lib/ |
{{MessageBox|1=Commandline|2=<pre> | {{MessageBox|1=Commandline|2=<pre> | ||
| Line 60: | Line 67: | ||
cd ~/mm/micro-manager1.4 | cd ~/mm/micro-manager1.4 | ||
./mmUnixBuild.sh | ./mmUnixBuild.sh | ||
| − | ./configure --with-imagej= | + | ./configure --with-imagej=/usr/local/ImageJ |
</pre>}} | </pre>}} | ||
| Line 82: | Line 89: | ||
=== Create the startup script === | === Create the startup script === | ||
| − | + | Micro-Manager requires the path to <code>/usr/lib/micro-manager</code>. Create the 4 line Bash script below in <code>/usr/local/ImageJ</code> and save it as, say, <code>mmscript</code>. | |
{{MessageBox|1=File: mmscript|2=<pre> | {{MessageBox|1=File: mmscript|2=<pre> | ||
Revision as of 13:01, 23 August 2013
Contents
Preparation
Install ImageJ
Download the Linux version of ImageJ from the NIH website and follow the installation instructions there. Test that ImageJ runs from a terminal:
Commandline
cd /usr/local/ImageJ/ ./run
Other Required Programs and Libraries
You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with:
Note
Heavy editing in progress: some dependencies may be missing
Commandline
sudo apt-get install subversion build-essential automake libtool \
libboost-all-dev zlib1g-dev swig sun-java6-sdk
You may also need to install additional packages (for cameras and special hardware). See the full list in #Dependencies
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
Add the Beanshell and SwingX to the ImageJ plugins directory:
Commandline
cd ~/mm/3rdpartypublic/classext sudo cp bsh-2.0b4.jar swingx-0.9.5.jar /usr/local/ImageJ/plugins/
Create a new micro-manager directory in /usr/lib/
Commandline
sudo mkdir /usr/lib/micro-manager
Building Micro-Manager
Create the Autotools files
configure uses the bundled version of ImageJ:
Commandline
cd ~/mm/micro-manager1.4 ./mmUnixBuild.sh ./configure --with-imagej=/usr/local/ImageJ
Compile
Commandline
make
Install
Commandline
sudo make install sudo ldconfig
Post Install
Create the startup script
Micro-Manager requires the path to /usr/lib/micro-manager. Create the 4 line Bash script below in /usr/local/ImageJ and save it as, say, mmscript.
File: mmscript
#!/bin/bash
cd /usr/local/ImageJ
export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
java -mx1200m \
-Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ \
-Dplugins.dir=/usr/local/ImageJ \
-cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar \
ij.ImageJ
Make the script executable:
Commandline
sudo chmod +x mmscript
Running Micro-Manager
Start ImageJ with your new script:
Commandline
./mmscript &
Run Plugins > Micro-Manager > Micro-Manager Studio
Appendix
Dependencies
| Name | Equivalent Synaptic package name |
|---|---|
| Required Dependencies: | |
| Subversion | subversion
|
| GNU C++ | build-essential
|
| GNU Autotools | automake
|
| GNU Libtool | libtool
|
| Boost libraries | libboost-all-dev
|
| zlib compression library | zlib1g-dev
|
| Simplified Wrapper and Interface Library | swig
|
| Sun Java SDK | sun-java6-sdk
|
| Optional Dependencies: | |
| Firewire Camera Library | libdc1394-*-dev
|
| Open Source Computer Vision Library | (FIXME) |