Download

The latest stable release of Change-O may be downloaded from PyPI or Bitbucket.

Development versions and source code are available on Bitbucket.

Installation

The simplest way to install the latest stable release of Change-O is via pip:

> pip3 install changeo --user

The current development build can be installed using pip and mercurial in similar fashion:

> pip3 install hg+https://bitbucket.org/kleinstein/changeo#default --user

If you currently have a development version installed, then you will likely need to add the arguments --upgrade --no-deps --force-reinstall to the pip3 command.

Linux

  1. The simplest way to install all Python dependencies is to install the full SciPy stack using the instructions, then install Biopython according to its instructions.

  2. Install presto 0.5.0 or greater.

  3. Download the Change-O bundle and run:

    > pip3 install changeo-x.y.z.tar.gz --user
    

Mac OS X

  1. Install Xcode. Available from the Apple store or developer downloads.

  2. Older versions Mac OS X will require you to install XQuartz 2.7.5. Available from the XQuartz project.

  3. Install Homebrew following the installation and post-installation instructions.

  4. Install Python 3.4.0+ and set the path to the python3 executable:

    > brew install python3
    > echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profile
    
  5. Exit and reopen the terminal application so the PATH setting takes effect.

  6. You may, or may not, need to install gfortran (required for SciPy). Try without first, as this can take an hour to install and is not needed on newer releases. If you do need gfortran to install SciPy, you can install it using Homebrew:

    > brew install gfortran
    

    If the above fails run this instead:

    > brew install --env=std gfortran
    
  7. Install NumPy, SciPy, pandas and Biopyton using the Python package manager:

    > pip3 install numpy scipy pandas biopython
    
  8. Install presto 0.5.0 or greater.

  9. Download the Change-O bundle, open a terminal window, change directories to the download folder, and run:

    > pip3 install changeo-x.y.z.tar.gz
    

Windows

  1. Install Python 3.4.0+ from Python, selecting both the options ‘pip’ and ‘Add python.exe to Path’.

  2. Install NumPy, SciPy, pandas and Biopython using the packages available from the Unofficial Windows binary collection.

  3. Install presto 0.5.0 or greater.

  4. Download the Change-O bundle, open a Command Prompt, change directories to the download folder, and run:

    > pip install changeo-x.y.z.tar.gz
    
  5. For a default installation of Python 3.4, the Change-0 scripts will be installed into C:\Python34\Scripts and should be directly executable from the Command Prompt. If this is not the case, then follow step 5 below.

  6. Add both the C:\Python34 and C:\Python34\Scripts directories to your %Path%. On Windows 7 the %Path% setting is located under Control Panel -> System and Security -> System -> Advanced System Settings -> Environment variables -> System variables -> Path.

  1. If you have trouble with the .py file associations, try adding .PY to your PATHEXT environment variable. Also, opening a command prompt as Administrator and run:

    > assoc .py=Python.File
    > ftype Python.File="C:\Python34\python.exe" "%1" %*