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Support #875

Install FlowCytometryTools on FreeBSD

Added by Daniel Curtis almost 4 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
Python
Target version:
Start date:
11/28/2016
Due date:
% Done:

100%

Estimated time:
0.50 h
Spent time:

Description

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

History

#1 Updated by Daniel Curtis almost 4 years ago

  • Status changed from New to In Progress
  • % Done changed from 0 to 50

#2 Updated by Daniel Curtis almost 4 years ago

  • Description updated (diff)

#3 Updated by Daniel Curtis almost 4 years ago

  • % Done changed from 50 to 90
  • Status changed from In Progress to Suspended
  • Description updated (diff)

#4 Updated by Daniel Curtis almost 4 years ago

  • % Done changed from 90 to 100
  • Status changed from Suspended to Resolved
  • Description updated (diff)

#5 Updated by Daniel Curtis almost 4 years ago

  • Description updated (diff)

#6 Updated by Daniel Curtis over 3 years ago

  • Status changed from Resolved to Closed

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