Installing Canopy

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Canopy works on modern Linux and MacOSX systems. No other systems are currently supported.

Canopy depends on some Python libraries and integrates several existing tools for sequence alignment and phylogenetic inference. To install Canopy, one should first download the Python code and then use the automated script to install the library dependencies.
Get the source distribution, untar it and cd into it:


curl -O
tar pxf canopy-0.1.4.tar.gz
cd canopy-0.1.4/


Next, use the setup script to install the Canopy module, the main application script and all python dependencies (everything assumes you are running Python 2.7.x). You need to have pip and setuptools installed. On Ubuntu Linux, these can be installed with commands:


sudo apt-get install python-pip
pip install setuptools


Then type either:


sudo python install


to install Canopy globally, or


python install --user


to install Canopy for a single user.

You can run test to check whether everything goes well:


canopy test


If all went well, you should see the following text:



or a python virtual environment existed:

Virtual environment is ready to launch by "source env/bin/activate"


Otherwise, it will show the missing Python libraries and give the suggestions:


Biopython(>=1.58) is not installed
Dendropy(==3.10.0) is not installed
Please choose:
  1. exit (Install the requirement libraries manually and then run the script again.)
  2. setup python virtual environment.
Your choice: [1/2]:


At the moment, you can choose ‘1’ to exit and install libraries manually. If you type ‘2’, then a virtual environment will be setup with the installation of library dependencies:


Your choice: [1/2]:2
Creating virtual environment
virtualenv env
source env/bin/activate
Installing python packages...
pip install numpy
pip install biopython>=1.58
pip install dendropy==3.10.0


After seeing the above text, a virtual Python environment has been set up in ./env.
The way you use the virtual environment is to type the following command (or include in a job script):

 $ source env/bin/activate 


If you need to add any other packages, use pip after you have activated the environment:

 $ pip install package_name 


If you want to restore your environment, just type:

 $ deactivate 


The installation is complete.