Installing Canopy

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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 from the Docker image.

1. Download (and rename) the image:

   docker pull veidenberg/canopy
   docker tag veidenberg/canopy canopy

   • Alternatively, you can build your own image from the Dockerfile in the Canopy source code package. For that, download/unpack the tarball (see step 1 in the guide below) and run the build command:

     docker build -t canopy .

   • The image contains preinstalled Canopy with all the dependencies.
   • Runs on all major operating systems, but requires Docker.
2. Run the image:

   docker run --rm -it -v "($pwd)/data:/results" canopy

   • The “-v” flag will provide a data folder for Canopy input/output ($pwd = current working directory).
   • Continue with the usage instructions. The example dataset is included with the image (or add your own to the specified data folder). Type “exit” when done.

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Install Canopy from the source code.

• Canopy source code is available form here.
• Prerequisites:
  • Python version 2.7.x
  • Python library dependencies:
    • Numpy (ver. 1.14.0)
    • Biopython (ver. 1.58)
    • Dendropy (ver. 3.10.0)
  • You can install these libraries manually (using pip) or use the Canopy installer script.

Install Canopy with the installer script.

• This will install the Canopy module, the main application script and all the library 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

1. Download Canopy, unpack it, and go to its directory:

   curl -O http://wasabiapp.org/download/canopy/canopy-0.1.5.tar.gz
   tar pxf canopy-0.1.5.tar.gz
   cd canopy-0.1.5/
   

   
   
2. Install Canopy, either globally:

   sudo python setup.py install

   
   or for a single user:

   python setup.py install --user

   
   
3. Test the new Canopy installation:

   canopy test

   
   
   • You should see the following confirmation text:
     

     Succeed!

     
     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:
     

     source env/bin/activate

     
     To exit the environment:
     

     deactivate

     
     
4. The installation is now complete. You are ready to run Canopy.