Created
March 23, 2019 08:00
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CellProfiler v3.1.8 conda environment
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| # run: conda env create -f environment.yml | |
| # run: conda env update -f environment.yml | |
| # run: conda env remove -n cellprofiler | |
| # This installs the v3.18 version of cellprofiler, which at the time of writing is the most recent stable release | |
| 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: | |
| - python=2.7 | |
| - appdirs | |
| - boto3 | |
| - cython | |
| - h5py | |
| - ipywidgets | |
| - openjdk | |
| - joblib | |
| - jupyter | |
| - libtiff | |
| - libxml2 | |
| - libxslt | |
| - lxml | |
| - packaging | |
| - pillow | |
| - pip | |
| - 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=3.0.2.0 | |
| - pip: | |
| - cellh5 | |
| - centrosome | |
| - inflect | |
| # - prokaryote==2.4.1 | |
| # - javabridge==1.0.18 | |
| # - python-bioformats==1.5.2 | |
| - git+https://github.com/CellProfiler/CellProfiler.git@v3.1.8 |
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