environment.yml

# run: conda env create -f environment.yml
# run: conda env update -f environment.yml
# run: conda env remove -n cpij-notebook
name: cellprofiler-notebooks
# in order of priority: lowest (top) to highest (bottom)
channels:
  - anaconda
  - goodman # mysql-python for mac
  - hanslovsky # imglib2-imglyb
  - damianavila82 # rise
  - bioconda
  - cyclus # java-jdk for windows
  - conda-forge # libxml2 for windows
dependencies:
  - appdirs
  - h5py
  - imglib2-imglyb
  - ipywidgets
  - java-jdk
  - jupyter
  - libtiff
  - libxml2
  - libxslt
  - lxml
  - mahotas
  - matplotlib!=2.1.0,>2.0.0
  - mysql-python
  - numpy
  - openjdk>=8.0.152
  - packaging
  - pandas
  - pillow
  - pip
  - python=2
  - pyzmq=15.3.0
  - requests
  - rise
  - scikit-image
  - scikit-learn
  - scipy
  - tifffile
  - pip:
    - centrosome
    - imagej
    - inflect
    - prokaryote==2.3.2
    - javabridge==1.0.15
    - python-bioformats==1.3.1
    - git+https://github.com/CellProfiler/CellProfiler.git@master