Posted 07 March, 2019
CellProfiler is not an easy to install tool; or perhaps I was clumsy on the first attempt (building from source) but I could not get it to work properly on a Linux machine; After another attempt using miniconda, I managed to get it running. This is just a documentation of how I got it working. In case I have to do it again. By no means am I an expert on the case.
I don’t know if these are all the dependencies but at some point I had to install them.
yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel bzip2 mariadb-devel libstdc++-devel gcc-c++ gtk2 ImageMagick ImageMagick-devel
Another issue is that the installation requires is libjbig.so.0 which can not be found, however jbigkit-libs provides libjbig.so.2.0; which can be soft-linked and it will then work;
cd /usr/lib64/ ln -s libjbig.so.2.0 libjbig.so.0
Get the latest version for Linux 64bit (or other) and make it executable; On Centos python 2.7 is default, and I believe it is required for CellProfiler.
wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh chmod 755 Miniconda2-latest-Linux-x86_64.sh
Finally we are ready to try the installation; Create a directory “cellprofiler” (not specific)
mkdir cellprofiler cd cellprofiler touch environment.yml
environment.yml should contain (using nano, vi, vim, emacs,…)
# run: conda env create -f environment.yml # run: conda env update -f environment.yml # run: conda env remove -n cellprofiler name: cellprofiler # in order of priority: highest (top) to lowest (bottom) channels: - anaconda - goodman # mysql-python for mac - bioconda - cyclus # java-jdk for windows - conda-forge # libxml2 for windows - BjornFJohansson # wxpython for linux dependencies: - appdirs - boto3 - cython - h5py - ipywidgets - java-jdk - joblib - jupyter - libtiff - libxml2 - libxslt - lxml - packaging - pillow - pip - python=2 - pyzmq=15.3.0 - mahotas - matplotlib!=2.1.0,>2.0.0 - mysqlclient - numpy - raven - requests - scikit-image>=0.13 - scikit-learn - scipy - sphinx - tifffile - wxpython=184.108.40.206 - pip: - cellh5 - centrosome - inflect - prokaryote==2.4.0 - javabridge==1.0.15 - python-bioformats==1.4.0 - git+https://github.com/CellProfiler/[email protected]
After this, make the environment; using : (will take a while)
conda env create -f environment.yml
While debugging you can also use : (to update)
conda env update -f environment.yml
This kinda works but generates two warnings that don’t seem to impact the tools (but perhaps I haven’t use specific functions that depend on these)
cellprofiler 3.1.8 has requirement prokaryote==2.4.1, but you'll have prokaryote 2.4.0 which is incompatible. cellprofiler 3.1.8 has requirement python-bioformats==1.5.2, but you'll have python-bioformats 1.4.0 which is incompatible.
Once that is finished, we can activate & run.
conda activate cellprofiler cellprofiler
Since this is on a server, I also needed to allow X11 forwarding over ssh;