GNet Solutions » GNU/Linux Administration

• Table of contents
• Prepare the Environment
• Install FlowCytometry with Pip
• Install FlowCytometryTools from GitHub
• Resources

This is a guide for setting up FlowCytometryTools on Arch Linux.

Prepare the Environment¶

• Make sure the system is up to date:
  

  pacman -Syyuu
  

• Install a few dependencies:
  

  pacman -S gcc-fortran-multilib git freetype2 pkgconf png
  

  
  NOTE: The multilib repository must be enabled in the pacman config file.
  NOTE: To use the FlowCytometryTools GUI, wxPython must be installed as well:
  

  pacman -S wxpython2.8
  

• Setup a Python development envirnoment, refer to issue #876

Install FlowCytometry with Pip¶

• Switch to the pydev user:
  

  su - pydev
  

• Create the FlowCytometryTools virtualenv:
  

  virtualenv2 FCT
  

• Activate the virtualenv:
  

  source ./FCT/bin/activate
  

• NOTE: If using the GUI utility, create a symbolic link of the host wxpython library in the virtualenv library:
  

  ln -s /usr/lib/python2.7/site-packages/wx.pth ~/venv/FCT/lib/python2.7/site-packages/
  

• Install FlowCytometryTools:
  

  pip --no-cache-dir install flowcytometrytools
  

  
  NOTE: I needed to install ipython inside the virtualenv, deactivate, then reactivate for the interactive shell to work:
  

  pip install ipython
  

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:
  

  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