top bar

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

(New page: == General remarks == We assume installation of ImageJ in "/usr/local/ImageJ". In addition to ImageJ and Micro-Manager, you need the following programmes: * svn for obtaining the reposit...)
 
 
(61 intermediate revisions by 12 users not shown)
Line 1: Line 1:
== General remarks ==
+
Intallation notes to install micro-manager from source on Ubuntu systems. These instructions can also be used without modifications for installations on [http://debian.org Debian systems] (tested on Debian Wheezy and Debian Jessy).
  
We assume installation of ImageJ in "/usr/local/ImageJ". In addition to ImageJ and Micro-Manager, you need the following programmes:
+
{{Note|These instructions are for Micro-Manager 1.4 and needs updates for Micro-Manager 2.0 (which uses JDK 8 and has source code on [https://github.com/micro-manager/micro-manager github] rather than in a subversion repository.}}
  
* svn for obtaining the repository
+
{{Note|This page has been updated for the build system changes of r13120, based on testing on Ubuntu 12.04 LTS.}}
* sun-java6-sdk or better/equivalent
+
* autoconf
+
* automake
+
* swig
+
* libace
+
* libace-dev
+
* g++
+
* libtool
+
  
In addition, note that:
+
See also: <code>doc/how-to-build.md</code> in the source tree.
  
* File versions might have changed, check before using the names given in the instructions.
+
= Preparation =
* Some operations have to be performed as "superuser" ("sudo …").
+
* Permissions of the new ImageJ directory might have to be set properly.
+
  
  
== Steps ==
+
== Install JDK ==
  
1. '''Installing ImageJ'''</p>
+
If you are building the Micro-Manager Java GUI, Java 1.6 or 1.7 is recommended[http://imagej.1557.x6.nabble.com/Java-error-when-compiling-a-plugin-tp5004378p5004386.html]. The simplest way is to use OpenJDK:
Get the Linux version of ImageJ from http://rsb.info.nih.gov/ij/download.html, move it to "/usr/local" and unpack it as described in http://rsb.info.nih.gov/ij/docs/install/linux.html. You will have a directory "/usr/local/ImageJ" with everything needed to run ImageJ (you can start ImageJ from the terminal: "cd /usr/local/ImageJ", followed by "./run").
+
2. '''Get Micro-Manager from the repository'''
+
  Make a directory somewhere (e.g. "~/src"), move to it ("cd ~/src") and get Micro-Manager with the command "svn checkout htpps://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3". This will download all the necessary files from the repository into "~/src/micromanager1.3/".
+
3. '''Beanshell and swingx'''
+
  Move to the new directory ("cd micromanager1.3") and copy beanshell and swingx from "~/src/micromanager1.3/classext" to the "plugins" directory of your ImageJ installation: "sudo cp classext/bsh-2.0b4.jar /usr/local/ImageJ/plugins" and "sudo cp classext/swingx-0.9.5.jar /usr/local/ImageJ/plugins".
+
4. '''Create a new micro-manager directory in /usr/lib'''
+
  "sudo mkdir /usr/lib/micro-manager"
+
5. '''mmUnixBuild.sh'''
+
  From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".
+
6. '''Run configure'''
+
  "./configure --with-imagej=/usr/local/ImageJ". You have to add the option (--with-imagej), because the default assumes a different localisation of ImageJ.
+
7. '''Run make'''
+
  "make"
+
8. '''Install as superuser'''
+
  "sudo make install"
+
9. Run '''ldconfig'''
+
  "ldconfig"
+
10. '''The starting script'''
+
    Starting ImageJ with the scripts provided in the ImageJ directory (run, script, see 1 above) will start ImageJ, but Micro-Manager, although now in the plugins directory, will not work properly because the path to /usr/lib/micro-manager is missing. Write your own script containing the 4 lines given below ("mmscript"), save and move it to /usr/local/ImageJ.
+
11. Running Micro-Manager cd to "/usr/local/ImageJ" and start ImageJ with your new script ("./mmscript &"). In the plugins menu of ImageJ, start Micro-Manager –> Micro-Manager Studio.
+
  
mmscript:
+
{{MessageBox|1=Commandline|2=<pre>
  
#!/bin/bash
+
sudo apt-get install openjdk-6-jdk
cd /user/local/ImageJ
+
</pre>}}
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
+
(You can also use <code>openjdk-7-jdk</code>.)
 +
 
 +
== Install ImageJ ==
 +
 
 +
[http://rsb.info.nih.gov/ij/download.html Download the Linux version of ImageJ] from the NIH website.  From a terminal, unzip to <code>/usr/local/</code>, and remove the embedded JRE, as we already have one installed.
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
cd ~/Downloads/
 +
sudo unzip ij*-linux*.zip -d /usr/local/
 +
sudo rm -rf /usr/local/ImageJ/jre
 +
sudo chmod a+Xr /usr/local/ImageJ
 +
</pre>}}
 +
 
 +
== Install Build Programs and Libraries ==
 +
 
 +
You will need a subversion client to checkout the source code, several libraries, and build tools.  Install them with:
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
sudo apt-get install subversion build-essential autoconf automake libtool \
 +
                    libboost-all-dev zlib1g-dev swig ant
 +
</pre>}}
 +
 
 +
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 <code>~/mm</code>. Besides the source tree, additional binary dependencies are stored in the <code>3rdpartypublic</code> repository.  The build scripts in the source tree assume <code>3rdpartypublic</code> is in the same parent folder level:
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
mkdir ~/mm
 +
cd ~/mm
 +
svn co https://valelab4.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
 +
svn co https://valelab4.ucsf.edu/svn/3rdpartypublic/
 +
</pre>}}
 +
 
 +
This creates 2 new folders in the <code>mm</code> directory:
 +
<pre>
 +
    ~/mm/micro-manager1.4
 +
    ~/mm/3rdpartypublic
 +
</pre>
 +
 
 +
Subversion (svn) will likely complain saying that it cannot verify the https certificate. Typing **t** to temporarily trust the certificate allows to retrieve the repository.
 +
 
 +
Also, when retrieving large repository (like the 3rdpartypublic/ repository), svn can hung in the middle of the process, with an error message:
 +
 
 +
<pre>
 +
svn: REPORT de '/svn/3rdpartypublic/!svn/vcc/default':
 +
Could not read chunk delimiter: Secure connection truncated (https://valelab4.ucsf.edu)
 +
</pre>
 +
 
 +
This can be [http://stackoverflow.com/questions/4031845/svn-resuming-aborted-checkout#13789596 solved] by typing:
 +
 
 +
{{MessageBox|1=Commandline|2=
 +
<pre>
 +
svn cleanup 3rdpartypublic/
 +
svn update 3rdpartypublic/ # This command might be executed several times
 +
</pre>}}
 +
 
 +
= Building Micro-Manager =
 +
 
 +
== Create the Autotools files ==
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
cd ~/mm/micro-manager1.4
 +
./autogen.sh
 +
./configure --enable-imagej-plugin=/usr/local/ImageJ
 +
</pre>}}
 +
 
 +
== Download build dependencies ==
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
make fetchdeps  # Required since SVN r14001-r14016
 +
</pre>}}
 +
 
 +
== Compile ==
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
make
 +
</pre>}}
 +
 
 +
== Install ==
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
sudo make install
 +
</pre>}}
 +
 
 +
= Post Install =
 +
 
 +
== Editing the startup script ==
 +
 
 +
A script named <code>mmimagej</code> will have been installed in <code>/usr/local/ImageJ</code>. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your <code>PATH</code>.
 +
 
 +
= Running Micro-Manager =
 +
 
 +
Start Micro-Manager by typing:
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
/usr/local/ImageJ/mmimagej 2>&1 >/dev/null &
 +
</pre>}}
 +
 
 +
To view the Core logging in the terminal while Micro-Manager is running, start simply as:
 +
 
 +
{{MessageBox|1=Commandline|2=<pre>
 +
 
 +
/usr/local/ImageJ/mmimagej
 +
</pre>}}
 +
 
 +
= Appendix =
 +
 
 +
== Dependencies ==
 +
 
 +
{| class="wikitable"
 +
|+ You need the following packages:
 +
! Name || Equivalent Synaptic package name
 +
|-
 +
|colspan="2"  style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"| Required Dependencies:
 +
|-
 +
| Subversion || <code>subversion</code>
 +
|-
 +
| GNU C++ || <code>build-essential</code>
 +
|-
 +
| GNU Autotools || <code>autoconf</code>, <code>automake</code>
 +
|-
 +
| GNU Libtool || <code>libtool</code>
 +
|-
 +
| Boost libraries || <code>libboost-all-dev</code>
 +
|-
 +
| zlib compression library || <code>zlib1g-dev</code>
 +
|-
 +
| Simplified Wrapper and Interface Library || <code>swig</code>
 +
|-
 +
| 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:
 +
|-
 +
| Python || <code>python-dev</code>, <code>python-numpy-dev</code>
 +
|-
 +
| Firewire Camera Library || <code>libdc1394-*-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
 +
|}
 +
 
 +
{{Programming_Sidebar}}

Latest revision as of 15:08, 12 March 2020

Intallation notes to install micro-manager from source on Ubuntu systems. These instructions can also be used without modifications for installations on Debian systems (tested on Debian Wheezy and Debian Jessy).

Note
These instructions are for Micro-Manager 1.4 and needs updates for Micro-Manager 2.0 (which uses JDK 8 and has source code on github rather than in a subversion repository.
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 ant

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://valelab4.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
svn co https://valelab4.ucsf.edu/svn/3rdpartypublic/

This creates 2 new folders in the mm directory:

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

Subversion (svn) will likely complain saying that it cannot verify the https certificate. Typing **t** to temporarily trust the certificate allows to retrieve the repository.

Also, when retrieving large repository (like the 3rdpartypublic/ repository), svn can hung in the middle of the process, with an error message:

svn: REPORT de '/svn/3rdpartypublic/!svn/vcc/default': 
Could not read chunk delimiter: Secure connection truncated (https://valelab4.ucsf.edu)

This can be solved by typing:

Commandline
svn cleanup 3rdpartypublic/
svn update 3rdpartypublic/ # This command might be executed several times

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
© Micro-Manager : Vale Lab, UCSF 2006-2011 | All Rights Reserved | Contact