Canopy is written in Python and integrates several existing tools for sequence alignment and phylogenetic inference. Canopy is provided as a downloadable package (works on Linux and MacOSX systems) and as a Docker image (works on all major operating systems).
Install Canopy as a Docker image:
- Download the Docker image from here.
- Includes preinstalled Canopy and all the dependencies.
- Compared to the source code installation, this option results in a larger download size and some virtualization overhead.
- Run the image with Docker.
Install Canopy from the source code:
- Download the package from here.
- Canopy requires Python version 2.7.x
- Install Python library dependencies:
- Numpy (ver. 1.16.6)
- Biopython (ver. 1.58)
- Dendropy (ver. 3.10.0)
- Install Canopy with the installer script.
- This will install the Canopy module, the main application script and all python dependencies.
- You need to have pip (preinstalled in Python 2.7.9+) and setuptools installed first.
On Ubuntu Linux, these can be installed with:
sudo apt-get install python-pip pip install setuptools
Download Canopy, unpack it, and go to its directory:
curl -O http://wasabiapp.org/download/canopy/canopy-0.1.4.tar.gz tar pxf canopy-0.1.4.tar.gz cd canopy-0.1.4/
Install Canopy, either globally:
sudo python setup.py install
or for a single user:
python setup.py install --user
Test the new Canopy installation:
You should see the following confirmation text:
or, if you installed to a Python virtual environment:
Virtual environment is ready to launch by "source env/bin/activate"
If some of the dependencies failed to install, you will be presented with the following options:
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]:
Here, you can select to install the listed libraries manually (option 1), or retry the automatic installation in Python virtual environment (option 2):
Your choice: [1/2]:2 Creating virtual environment virtualenv env Activating... source env/bin/activate Installing python packages... pip install numpy pip install biopython==1.58 pip install dendropy==3.10.0
After this, a virtual Python environment has been set up in ./env directory.
Enter the environment to use Canopy:
To exit the environment:
- You should see the following confirmation text:
The installation is now complete. You are ready to run Canopy.