install cellprofiler into a conda env on eddie

install_cellprofiler.sh

#!/bin/bash

# script to install cellprofiler into a conda environment
# named 'cellprofiler'
#
# to activate this environment you will need to load anaconda/4.3.1
# then run
#>>>      source activate cellprofiler

# load anaconda
module load anaconda/4.3.1

# create an environment file and save it as 'environment.yml'
# in the current directory
cat <<EOT >> environment.yml
# to remove run: conda env remove -n cellprofiler
name: cellprofiler
# in order of priority: lowest (top) to highest (bottom)
channels:
  - anaconda
  - bjornfjohansson # for wxpython on linux
  - goodman # mysql-python for mac
  - bioconda
  - cyclus # java-jdk for windows
  - conda-forge # libxml2 for windows
dependencies:
  - appdirs
  - cython
  - h5py
  - ipywidgets
  - java-jdk
  - jupyter
  - libtiff
  - libxml2
  - libxslt
  - lxml
  - packaging
  - pillow
  - pip
  - python=2
  - pyzmq=15.3.0
  - mahotas
  - matplotlib!=2.1.0,>2.0.0
  - mysql-python
  - numpy
  - raven
  - requests
  - scikit-image
  - scikit-learn
  - scipy
  - sphinx
  - tifffile
  - wxpython
  - wxpython=3.0.2.0
  - pip:
    - cellh5
    - centrosome
    - inflect
    - prokaryote==2.3.2
    - javabridge==1.0.15
    - python-bioformats==1.3.1
    - git+https://github.com/CellProfiler/[email protected]
EOT

# call conda to create this environment from the environment.yml
# file we just created
conda env create -f environment.yml
conda env update -f environment.yml

exit 0