Source installation (OS X and macOS)

Anne Carpenter edited this page Jul 27, 2018 · 10 revisions

Table of Contents

  1. Installation
  2. Usage

Installation

Homebrew

Install Homebrew:

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Java

$ brew cask install java

MySQL

Install MySQL:

$ brew install mysql

Python

Install Python:

$ brew install python@2

wxPython

Install wxPython:

$ brew install wxpython

pip

NumPy

$ pip2 install cython matplotlib numpy scipy

CellProfiler

Install CellProfiler:

$ git clone https://github.com/CellProfiler/CellProfiler.git $HOME/CellProfiler

$ pip2 install --editable $HOME/CellProfiler

(Note, if you get the NameError: name 'sys_platform' is not defined error at this point, you can try

$ pip2 uninstall distribute
$ pip2 install setuptools

Usage

Running CellProfiler

$ cellprofiler

Running CellProfiler’s test suite:

$ cd $HOME/CellProfiler

$ python setup.py test

Packaging CellProfiler:

$ cd $HOME/CellProfiler

$ python setup.py py2app
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