CentOS7: administrator version

These instructions are for CentOS7 on a high-performance computer cluster, such as the HPC at the UMC Utrecht.

Note: the instructions below require full administration rights.

Update and prepare

To make installing easier, we will add the current user to the sudoers file, this makes it possible to run sudo. Replace USERNAME with your username.

sudo adduser USERNAME sudo

The system must be up-to-date. Install updates, answer --yes to everything. Make sure you stay on CentOS version 6.6 as this guide is meant for CentOS 6.6 only. This can take a while.

su -c 'yum -y update'

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

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

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

Install required libraries and packages using apt-get

Let's first check whether some packages are installed already.

for PACK in curl cvs gcc gcc-c++ gimp git libtool openjpeg perl svn vim wget giflib-devel libjpeg-devel libtiff-devel libpng-devel freetype-devel; do echo "* checking [ "$PACK" ]...."; command -v "$PACK"; echo "---------"; echo ""; done

Now you can just install the packages that returned empty. In our case, we will install the remaining important packages (and their dependencies) we need. First we update the yum Repodata cache.

yum makecache fast

su -c 'yum -y install autoconf automake cmake gcc-c++ \
    gimp openjpeg giflib-devel libjpeg-devel libtiff-devel libpng-devel freetype-devel'

Install wmctrl

Install the latest version of wmctrl.

yum install wmctrl

Install zbar

Install the latest version of zbar.

yum install zbar

Install parallel

Install the latest version of GNU Parallel. First create and go to the src directory, then download and extract parallel.

mkdir -p ~/src && cd ~/src && \\
    wget http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2 && \
	tar jxf parallel-latest.tar.bz2 && \
	rm parallel-latest.tar.bz2

Install parallel

cd ~/src/parallel-*

./configure && make && su -c "make install" && make clean

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 && su -c "make install" && make clean

Install libtiff

Install the latest libtiff library using cvs. When cvs asks for a password for the anonymous login, just press enter. 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 && su -c "make install" && make clean

Install JPEG2000

mkdir -p ~/svn && cd ~/svn

svn checkout http://openjpeg.googlecode.com/svn/trunk/ openjpeg

Install openjpeg.

cd ~/svn/openjpeg

cmake . && make && su -c "make install" && make clean

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 && su -c "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

Install openslide [openjpeg not found error]

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 && su -c "make install" && make clean

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/

Install datamatrix barcode libraries [error: dmtx lib not found]

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 && su -c "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 && su -c "make install" && make clean

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/swvanderlaan/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/

Install CellProfiler

Instructions for CentOS 6 taken from on cellprofiler.org.

Create repository file for yum.

mkdir -p /etc/yum.repos.d && \
if ! [[ -f /etc/yum.repos.d/cellprofiler.repo ]] ; then \
    su -c 'printf "\n[cellprofiler]\n\
name=CellProfiler for CentOS 6\n\
baseurl=http://www.cellprofiler.org/linux/centos6/\n\
enabled=1\n\
gpgcheck=0\n" > /etc/yum.repos.d/cellprofiler.repo';
    fi

Install CellProfiler using yum.

su -c 'yum -y install cellprofiler'

Cleanup, restart & you're done!

Fix linked libraries.

sudo ldconfig

Restart.

sudo reboot