changeo 0.3.0

Requirements

• Python 3.4.0

• setuptools 2.0

• NumPy 1.8

• SciPy 0.14

• pandas 0.15

• Biopython 1.65

• presto 0.5

• MUSCLE v3.8

Installation - 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 from here.

3. Extract the Change-O bundle and run:

   > python3 setup.py install --user

Installation - 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. Unzip the Change-O bundle, open a Command Prompt, change directories to the Change-O folder, and run:

   > python setup.py install.

4. For a default installation of Python 3.4, the Change-O 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.

5. 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.

Installation - Mac OS X

1. Install Xcode 3.2.6 Available from the Apple store or developer downloads. If you have a newer version (eg, Xcode 4.6.3) that will work also, but Xcode 3 is free of charge. If Xcode fails to install with an “Unknown Error”, change the date on your system to some time in 2011, install Xcode, and then change the date back to the proper setting.

2. Install XQuartz 2.7.5 Available from the XQuartz project.

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

4. Open a terminal and install gfortran (required for SciPy) using Homebrew (this can take an hour to install):

   > brew install gfortran

   If the above fails run this instead:

   > brew install --env=std gfortran
5. Install Python 3.4.0+ and set the path to the python3 executable:

   > brew install python3

   > echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profile

   Exit and reopen the terminal application so the PATH setting takes effect
6. Install NumPy, SciPy, pandas and Biopyton using the Python package manager:

   > pip3 install numpy scipy pandas biopython
7. Extract the Change-O bundle, open a terminal window, change directories to the Change-O folder, and run:

   > python3 setup.py install