Ubuntu 12.04 - swvanderlaan/slideToolKit GitHub Wiki

In the past we provided instructions to install slideToolKit and CellProfiler on a Ubuntu 12.04 LTS system; you can find these here for legacy purposes. In principle, given the right Ubuntu setup, these should still work.

Step 1 - Update and prepare

The system must be up-to-date. Install updates, answer --yes to everything. Make sure you stay on version 12.04 and do not upgrade to Ubuntu 14 (Trusty Tar). This can take a while.

sudo apt-get --yes update && sudo apt-get --yes upgrade && \ 
    sudo apt-get --yes dist-upgrade && sudo apt-get --yes autoremove

Binairies are executed from your local bin folder. Create your ~/bin and add it to your PATH if needed.

if ! [ "$PATH" =~ (:$HOME/bin:](/swvanderlaan/slideToolKit/wiki/:~/bin:)-) ; then \
	mkdir -p ~/bin && \
	printf "\n# Add ~/bin to your PATH\nexport PATH=\"~/bin:\$PATH\" \n" >> ~/.profile
	fi

On Ubuntu Linux you need to reboot for the PATH to be found.

sudo reboot

Now we are up to date, and ready to continue the installation.

Step 2 - Install required libraries and packages using apt-get

This apt-get oneliner will install most of the important packages we need and takes take of most dependencies as well.

sudo apt-get --yes update && sudo apt-get --yes install autoconf \
    automake "build-essential" curl cvs gimp git "libgtk2.0-dev" \
    "libjpeg-dev" "libopenjpeg-dev" "libopenslide-dev" "libsqlite3-dev" \
    libtool "libxml2-dev" parallel perl "pkg-config" vim wget wmctrl \
    "zbar-tools"

Most dependcies are now installed, but we need some more.

Step 3 - Install zlib

Install the latest zlib compression libraries. First create and go to the src directory, then download and extract zlib.

mkdir -p ~/src && cd ~/src && \\
    wget http://zlib.net/zlib-1.2.8.tar.gz -O zlib-1.2.8.tar.gz && \
	tar xzvf zlib-1.2.8.tar.gz && \
	rm zlib-1.2.8.tar.gz

Install zlib.

cd ~/src/zlib-1.2.8

./configure && make && sudo make install && make clean

Step 4 - Install libtiff

Install the latest libtiff library using cvs. When cvs asks for a password for the anonymous login, just press enter. The funny thing is, apt-get install libtiff4 does install libtiff 3.9.* . But we need libtiff 4.* for BigTIFF support. First create and go to the cvs directory, then download and extract libtiff.

mkdir -p ~/cvs && cd ~/cvs

cvs -d :pserver:cvsanon:@cvs.maptools.org:/cvs/maptools/cvsroot checkout libtiff

Install libtiff.

cd ~/cvs/libtiff

./configure && make && sudo make install && make clean

Step 5 - Install ImageMagick

Download and install the latest version ImageMagick from there website. First create and go to the src directory, then download and extract ImageMagick.

mkdir -p ~/src/ && cd ~/src

wget http://www.imagemagick.org/download/ImageMagick.tar.gz -O ImageMagick.tar.gz && \
	tar xzfv ImageMagick.tar.gz && \
	rm ImageMagick.tar.gz

Install ImageMagick.

cd ~/src/ImageMagick*

./configure && make && sudo make install && make clean

After the ImageMagick installation we need to examine the libraries, update links and cache where necessary. Else ImageMagick would work properly.

sudo ldconfig /usr/local/lib

Step 6 - Install openslide

Download the latest version of openslide from github. Pull if already exists; clone if none existing. First create and go to the git directory, then download the source.

mkdir -p ~/git/ && cd ~/git

if [ -d ~/git/openslide/.git ]; then \
		cd ~/git/openslide && git pull; \
	else \
		cd ~/git/ && git clone git://github.com/openslide/openslide.git; \
	fi

Install openslide.

cd ~/git/openslide

autoreconf -i

./configure && make && sudo make install && make clean

Step 7 - Install bfconvert

Download and install the latest version of bfconvert. First create and go to the usr directory, then download and extract bftools.

mkdir -p ~/usr && cd ~/usr

wget http://downloads.openmicroscopy.org/latest/bio-formats5/artifacts/bftools.zip && \
    unzip -o bftools.zip && \
    rm bftools.zip

No need to configure the bftools. We only need to add symbolic links in ~/bin, this will make the BioFormats availabe within your PATH. Adding the bftools to your PATH is obligatory for the slideToolkit to find its dependencies.

mkdir -p ~/bin/ && ln -s -f -v ~/usr/bftools/bfconvert ~/bin/ && \
    ln -s -f -v ~/usr/bftools/domainlist ~/bin/ && \
    ln -s -f -v ~/usr/bftools/formatlist ~/bin/ && \
    ln -s -f -v ~/usr/bftools/ijview ~/bin/ && \
    ln -s -f -v ~/usr/bftools/mkfake ~/bin/ && \
    ln -s -f -v ~/usr/bftools/showinf ~/bin/ && \
    ln -s -f -v ~/usr/bftools/tiffcomment ~/bin/ && \
    ln -s -f -v ~/usr/bftools/xmlindent ~/bin/ && \
    ln -s -f -v ~/usr/bftools/xmlvalid ~/bin/

Step 8 - Install datamatrix barcode libraries

Download and install the latest version of the datamatrix barcode libraries and binairies (dmtx) from sourceforge using git. First create and go to the git directory, then download and extract the libraries.

mkdir -p ~/git/ && cd ~/git

if [ -d ~/git/libdmtx/.git ]; then \
		cd ~/git/libdmtx && git pull; \
	else \
		cd ~/git/ && git clone git://libdmtx.git.sourceforge.net/gitroot/libdmtx/libdmtx; \
	fi

Install the datamatrix barcode libraries

cd ~/git/libdmtx && mkdir -p m4 && autoreconf --force --install

./configure && make && sudo make install && make clean

Now the binairies. First create and go to the git directory, then download and extract the binairies.

mkdir -p ~/git/ && cd ~/git

if [ -d ~/git/dmtx-utils/.git ]; then \
		cd ~/git/dmtx-utils && git pull; \
	else \
		cd ~/git/ && git clone git://git.code.sf.net/p/libdmtx/dmtx-utils; \
	fi

Install the datamatrix barcode binairies.

cd ~/git/dmtx-utils && mkdir -p m4 && autoreconf --force --install

./configure && make && sudo make install && make clean

Step 9 - Install slideToolkit

Download and install the latest version of the slideToolkit from github. First create and go to the git directory, then download the slideToolkit.

mkdir -p ~/git/ && cd ~/git

if [ -d ~/git/slideToolkit/.git ]; then \
		cd ~/git/slideToolkit && git pull; \
	else \
		cd ~/git/ && git clone https://github.com/bglnelissen/slideToolkit.git; \
	fi

Add symbolic links in ~/bin/. Now the slideToolkit will be availabe in your PATH. Adding the slideToolkit tools to your PATH makes it easier to acces the slideToolkit commands.

mkdir -p ~/bin/ && ln -s -f -v ~/git/slideToolkit/slide* ~/bin/

Step 10 - Install CellProfiler

We have no step-by-step installation instructions for CellProfiler yet. But you can follow the instructions on cellprofiler.org, or on the CellProfiler github wiki page.

You can also try the 'Docker' version of CellProfiler, which is known to work with Ubuntu and can be found here.

Step 11 - Cleanup, restart & you're done!

Fix linked libraries.

sudo ldconfig

Restart.

sudo reboot