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 git in similar fashion:
> pip3 install git+https://bitbucket.org/kleinstein/changeo@master --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.
Requirements¶
The minimum dependencies for installation are:
Some tools wrap external applications that are not required for installation. Those tools require minimum versions of:
AlignRecords requires MUSCLE 3.8
ConvertDb-genbank requires tbl2asn
AssignGenes requires IgBLAST 1.6, but version 1.11 or higher is strongly recommended.
BuildTrees requires IgPhyML 1.0.5
Linux¶
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.
Install presto 0.6.2 or greater.
Download the Change-O bundle and run:
> pip3 install changeo-x.y.z.tar.gz --user
Mac OS X¶
Install Xcode. Available from the Apple store or developer downloads.
Older versions Mac OS X will require you to install XQuartz 2.7.5. Available from the XQuartz project.
Install Homebrew following the installation and post-installation instructions.
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.
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
Install NumPy, SciPy, pandas and Biopython using the Python package manager:
> pip3 install numpy scipy pandas biopython
Install presto 0.6.2 or greater.
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¶
Install Python 3.4.0+ from Python, selecting both the options ‘pip’ and ‘Add python.exe to Path’.
Install NumPy, SciPy, pandas and Biopython using the packages available from the Unofficial Windows binary collection.
Install presto 0.6.2 or greater.
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
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 6 below.Add both the
C:\Python34
andC:\Python34\Scripts
directories to your%Path%
. On both Windows 7 and Windows 10, the%Path%
setting is located under Control Panel -> System and Security -> System -> Advanced System Settings -> Environment variables -> System variables -> Path.If you have trouble with the
.py
file associations, try adding.PY
to yourPATHEXT
environment variable. Also, try opening a Command Prompt as Administrator and run:> assoc .py=Python.File > ftype Python.File="C:\Python34\python.exe" "%1" %*