Conda environment file for CellProfiler

environment.yml

# See https://github.com/CellProfiler/CellProfiler/wiki/Conda-Installation
#
# conda env create -f environment.yml 
# source activate cellprofiler-master
# cellprofiler

name: cellprofiler-master
# in order of priority: lowest (top) to highest (bottom)
channels:
#  - goodman # mysql-python for mac
  - bioconda
#  - cyclus # java-jdk for windows
#  - conda-forge # libxml2 for windows
dependencies:
  - python=2
  - jupyter
  - ipywidgets
  - matplotlib
  - wxpython
  - lxml
  - libxml2
  - libxslt
  - cython
  - mysql-python
#  - mahotas
  - numpy
  - scipy
  - pyzmq
  - h5py
  - java-jdk
  - pillow
  - javabridge
  - pip
  - pip:
    - python-bioformats
    - centrosome
    - prokaryote
    - "--editable=git+https://github.com/scikit-image/scikit-image.git@master#egg=scikit-image-0.13.0dev"
    - "--editable=git+https://github.com/CellProfiler/CellProfiler.git@master#egg=cellprofiler-master"