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This note was written using Revision: 2580 (https://valelab.ucsf.edu/trac/micromanager/timeline) that contained fixes to linux build by Nico and debian-specific scripts by Johan. Following notes are a log of things I needed to do for building the deb packages successfully and running micro-manager. Suggestions were provided by Martin and Johan. Search "non-hardware micro-manager setup on linux" thread in micro-manager-general list. These steps will be out-of-date sooner rather than later, but should provide an idea of overall process.

OS was Ubuntu jaunty.

--[[User:Sanguine|Shalin]] 12:44, 2 June 2009 (UTC)
== Pre-requisite packages ==


- ImageJ (either debian package or uncompress tar.gz from ImageJ website in /usr/local/ImageJ/). The debs on launchpad are version 1.41n whereas you can get the latest from the ImageJ website. Micro-manager plugin requires ImageJ version 1.42n and above.

- sun-java6-jdk

-libtool

-libace-5.6.3

-libace-dev 

-libswingx-java (ver. 0.9.2) 

-libusb-0.1-4 

-libusb-dev

-autoconf

-automake

-swig

-g++

-bsh


More or less packages may be required. Above was what I needed to install.

== After all is setup, cd to directory of choice and get SVN copy of micro-manager ==

$svn co   https://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3 

I received Revision 2580.

== Bootstrap the autobuild tools. ==
$./mmUnixBuild.sh 

== Configure and build ==
$./configure  --with-imagej=/usr/local/ImageJ (Replace the path suitably)

$make

* Errors encountered during make:

1. In USBManager.

<nowiki>
*** Warning: Linking the shared library libmmgr_dal_USBManager.la against the

*** static library /usr/lib/libusb.a is not portable!

libtool: link: g++ -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.3.3/crtbeginS.o  .libs/USBManager.o   ../../MMDevice/.libs/libMMDevice.a /usr/lib/libusb.a -L/usr/lib/gcc/x86_64-linux-gnu/4.3.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.3.3/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib/crtn.o    -Wl,-soname -Wl,libmmgr_dal_USBManager.so.0 -o .libs/libmmgr_dal_USBManager.so.0.0.0

/usr/bin/ld: /usr/lib/libusb.a(usb.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC

/usr/lib/libusb.a: could not read symbols: Bad value

collect2: ld returned 1 exit status

make[2]: *** [libmmgr_dal_USBManager.la] Error 1

make[2]: Leaving directory `/home/sanguine/research/umanager/micromanager1.3/DeviceAdapters/USBManager'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/home/sanguine/research/umanager/micromanager1.3/DeviceAdapters'

make: *** [all-recursive] Error 1

</nowiki>

* Resolved by deleting references to USBManager in DIST_SUBDIR variable inside DeviceAdapters/Makefile.

* Compilation succeded!! 

== If not making debian packages, do $make install and you should be fine. I haven't tried it yet. ==

== Making debian packages. The path I chose for easy management of files.==
* Modify newImageJ script inside portdebian directory.
  ij_path=/usr/local/ImageJ 

  Substitute all references to /usr/share/imagej by /usr/local/ImageJ 

* Modify debiancontrol.port inside portdebian directory.
  Architecture: amd64 in debiancontrol.port .

* Modify mkdebian.sh inside portdebian
  Substitute all references to /usr/share/imagej by /usr/local/ImageJ   

  Include configuration, html, and xml acquisition samples inside the package.
  <nowiki> ##### Programs </nowiki>
  mkdir -p $ROOTBIN/usr/bin/
  cp Test_Serial/mm_testserial ModuleTest/mm_moduletest Test_MMCore/mm_testCore $ROOTBIN/usr/bin/
  strip $ROOTBIN/usr/bin/*
  <nowiki> ##### And configuration files </nowiki>
  cp bin/*.cfg $ROOTBIN/usr/bin/
  cp bin/*.html $ROOTBIN/usr/bin/
  cp bin/*.xml $ROOTBIN/usr/bin/




* Then do $./portdebian/mkdebian.sh

Got error: cp: cannot stat `Tracking/Tracker_.jar': No such file or directory

Error resolved by $cd Tracking, $make. Somehow earlier make had missed it.

* Two packages micromanager.deb and micromanager-ij.deb are created in top directory of the source tree. Install them.

$ dpkg -i micromanager micromanager-ij worked.

* imagejmm script created by micromanager-ij works, however doesn't bring up micro-manager. You need to invoke it from Plugins-> Micro-manager -> Micro-manager Studio.