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This is a guide for setting up FlowCytometryTools on FreeBSD 10.

WARNING: FlowCytometryTools currently fails while building the numpy dependency. Your mileage may vary.

Prepare the Environment¶

• Make sure the system is up to date:
  

  pkg update && pkg upgrade
  

• Install a few dependencies:
  

  pkg install atlas gcc46 git freetype2 pkgconf png py27-matplotlib
  

NOTE: To use the FlowCytometryTools GUI, wxPython must be installed as well:

pkg install py27-wxPython28

• NOTE: Matplotlib failed to build due to an incorrect header include directory path, creating a link to the /usr/include directory fixed the problem:
  

  ln -s /usr/local/include/freetype2/ft2build.h /usr/include/
  

• Setup a Python development envirnoment, refer to issue #874

Install FlowCytometry with Pip¶

• Switch to the pydev user:
  

  su - pydev
  

• Create the FlowCytometryTools virtualenv:
  

  virtualenv FCT
  

• Activate the virtualenv:
  

  source ./FCT/bin/activate
  

• Install flowcytometrytools using pip:
  

  env CC=gcc46 CXX=g++46 CPP=cpp46 pip install flowcytometrytools
  

  
  NOTE: flowcytometrytools must be compiled using GCC 4.6 due to fortran support.

Install FlowCytometryTools from GitHub¶

• Switch to the pydev user:
  

  su - pydev
  

• Create the FlowCytometryTools virtualenv:
  

  virtualenv FCT
  

• Activate the virtualenv:
  

  source ./FCT/bin/activate
  

• Clone the FlowCytometryTools from GitHub:
  

  git clone https://github.com/eyurtsev/FlowCytometryTools.git
  cd FlowCytometryTools
  

• Run the install script:
  NOTE: FlowCytometryTools must be compiled using gcc46
  

  env CC=gcc46 CXX=c++46 CPP=cpp46 python setup.py install
  

Resources¶

• https://github.com/eyurtsev/FlowCytometryTools
• https://pypi.python.org/pypi/FlowCytometryTools
• http://eyurtsev.github.io/FlowCytometryTools/install.html
• http://eyurtsev.github.io/FlowCytometryTools/tutorial.html