Installation

Dependencies

  • Python is needed. phyloExpCM has been tested with Python 2.6 and 2.7 on Linux and Mac OS X, but will probably work with earlier versions as well.
  • phyloExpCM uses mapmuts. It has been tested with version 1.0.
  • phyloExpCM interfaces with codonPhyML. It has been tested with version 1.00 201306.18 on Mac OS X and Linux.
  • phyloExpCM interfaces with HYPHY. It has been tested with versions 2.112* for Mac OS X and for Linux.
  • Some of the scripts and functions in phyloExpCM use numpy. It has been tested with numpy version 1.6.1.
  • Some of the scripts and functions in phyloExpCM use matplotlib. It has been tested with matplotlib version 1.3.1.

Installation

To install phyloExpCM, first download the source ZIP repository on GitHub. After unzipping the file, run the following commands:

cd phyloExpCM
python setup.py build
python setup.py install

The last command might require you to use:

sudo python setup.py install

if you do not have privileges to the default installation directory, or:

python setup.py install --user

if you want to install locally.

These commands install the Python modules and also install several scripts, which provide the most convenient high-level interface into the package.

HYPHY include files

Several HYPHY include batch files (.ibf files) are distributed with this package as they are necessary to run some of the HYPHY analyses. These are in the ./src/data/ subdirectory in the package source. If you install the package using the commands above, these data files should be installed in a location that the scripts are able to find. If you run the package without installing it fully, however, the scripts may not be able to find these files. In that case, you will get errors from HYPHY indicating that it cannot find specified include files.