Emperor is a python package hosted in GitHub that relies on NumPy, scikit-bio and qcli. These packages must be installed prior running the setup.py
script.
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To clone the git repository directly into your machine:
git clone git://github.com/biocore/emperor.git
To perform a global installation of Emperor, execute the following command from a terminal session:
python setup.py install
If you do not want to do a global installation, you will have to add the Emperor scripts and libraries to the PATH
and PYTHONPATH
environment variables. To add these variables to your .bash_profile
issue the following terminal commands:
echo "export PATH=$HOME/emperor_bin/:$PATH" >> ~/.bash_profile
echo "export PYTHONPATH=$HOME/emperor_lib/:$PYTHONPATH" >> ~/.bash_profile
python setup.py install --install-scripts=~/emperor_bin/ --install-purelib=~/emperor_lib/ --install-lib=~/emperor_lib/
Alternatively Emperor can be installed from the Python Package Index (PyPi) using either conda (note that this method will be notably faster):
conda install scikit-bio
pip install emperor
or using pip:
pip install numpy
pip install emperor
To test for a correct installation, open a new terminal window and issue the following command to see the help of make_emperor.py
:
make_emperor.py -h
Usage: make_emperor.py [options] {-i/--input_coords INPUT_COORDS -m/--map_fp MAP_FP}
[] indicates optional input (order unimportant)
{} indicates required input (order unimportant)
This script automates the creation of three-dimensional PCoA plots to be visualized with Emperor using Google Chrome.
Example usage:
Print help message and exit
make_emperor.py -h
...