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Conda imagemagic11/24/2023 ![]() While debugging you can also use : (to update) conda env update -f environment.yml 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,…) this, make the environment using : (will take a while) 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. NameError: name 'TractSeg' is not definedįile "/home/amitjc/.local/bin/TractSeg", line 20, in įile "/home/amitjc/.local/lib/python3.7/site-packages/tractseg/libs/plot_utils.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. Type "help", "copyright", "credits" or "license" for more information. How to make it work from Default (base) commandline? Because I need to run TractSeg, which depends on pytorch. Sudo apt install imagemagick-6.q16hdri # version 8:6.9.10.23+dfsg-2.1ubuntu3.1īash: syntax error near unexpected token `('īash: syntax error near unexpected token `x' Sudo apt install graphicsmagick-imagemagick-compat # version 1.4+really1.3.33+hg16115-1, or (base) from _future_ import print_functionĬommand 'import' not found, but can be installed with: Successfully installed pillow-7.1.1 torch-1.4.0+cpu torchvision-0.5.0+cpu Installing collected packages: torch, pillow, torchvision (base) pip install torch=1.4.0+cpu torchvision=0.5.0+cpu -f ![]() ![]() However, on attempting verification as metioned on the Get-Started page, Iget error messages which can be found below.Īmit. I have installed pytorch using conda as well as pip command on ubuntu 19.10 with non-CUDA GPU.
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