Once that is finished, we can activate & run. 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.Ĭellprofiler 3.1.8 has requirement python-bioformats=1.5.2, but you'll have python-bioformats 1.4.0 which is incompatible. While debugging you can also use : (to update) conda env update -f environment.yml natural contrast, or is stained will work well for bright field. # in order of priority: highest (top) to lowest (bottom)Īfter this, make the environment using : (will take a while) conda env create -f environment.yml If the object of interest does not naturally absorb light, a stain that does absorb. Even though in the CellProfiler wiki page for installation on Ubuntu 20.04 is. # run: conda env update -f environment.yml Its not a command that you run by itself. wget Ĭhmod 755 Miniconda2-latest-Linux-x86_64.sh Install CellProfilerįinally we are ready to try the installation Create a directory “cellprofiler” (not specific) mkdir cellprofilerĮnvironment.yml should contain (using nano, vi, vim, emacs,…) # run: conda env create -f environment.yml 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. yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel bzip2 mariadb-devel libstdc++-devel gcc-c++ gtk2 ImageMagick ImageMagick-develĪnother 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/ I don’t know if these are all the dependencies but at some point I had to install them. This is just a documentation of how I got it working. Install CellProfiler on Centos 7.6 using conda.ĬellProfiler 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.
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