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Tutorial: Install and set up Epiphyte

Requirements:

  • either a configured VM (tutorial 1) or local machine running Linux
  • 400 MB free disk space
  • Python 3 and Anaconda (or Miniconda)

Note: if using Windows, we highly recommended using VS Code for this tutorial.

Once your MySQL database (and your optional additional storage) is configured, you're ready to install and set up Epiphyte!

The database can be defined and structured remotely from a client computer, separate from where the database is hosted (e.g. on a remote server or virtual machine). This means you can install and configure Epiphyte on a separate computer (e.g., a workstation or personal laptop), while gaining the power and storage capacity of an external server. A schematic of this arrangement is given below:

Infrastructure diagram

Here, the VM (configured by you, the dev user) hosts the database, while the codebase controls and populates it with data. Once you install and configure Epiphyte, it's possible to directly interact with the remotely-hosted database from your PC or workstation.

In this tutorial we'll go through how to install and set up Epiphyte on your PC, workstation, or whichever machine you'll use for interacting with the data.

There are two ways to install Epiphyte: either via pip or by cloning the GitHub repository. We'll cover both methods, but if you already cloned the repo and are going through the tutorials locally, skip to that section.

Installing Epiphyte via pip

Create a new conda environment suitable for the Epiphyte requirements:

conda create --name epiphyte python=3.9.18 ipython

Activate the conda environment and install Epiphyte:

conda activate epiphyte
pip install epiphyte

Installing Epiphyte via git

Clone the repository, and change your directory to the repository: 

git clone git@github.com:mackelab/epiphyte.git
cd epiphyte

Create a new conda environment suitable for the Epiphyte requirements:

conda create --name epiphyte python=3.9.18 ipython

Activate the conda environment and install the dependencies:

conda activate epiphyte
pip install -e .

Verify the installation:

conda list