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 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)
You can install the 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 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
```
1. 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/
```
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
```
The installation is now complete. You are ready to run Canopy.