Local Machine Installation

Requirements:

• OS: Linux or Mac/OSx
• Python 3.5 or higher (either system-level, or in an IDE)
• 400 MB free disk space
• Permission to perform sudo-level commands

Installation:

Installing epiphyte involves three broad steps: 1) installing and setting up a DataJoint docker container on the system-level, 2) download and launch the DataJoint MySQL server via docker-compose, and 3), installing the code package either on the system-level, or within a virtual environment (recommended). More information about the packages and software used by epiphyte can be found in the wiki.

1. Install and set-up the DataJoint docker container.

• Install the correct Docker for your OS.
• Verify the Docker installation:

docker --version
docker run hello-world

• Install Docker Compose.
• Verify the Docker Compose installation:

docker-compose --version

2. Download and launch the DataJoint MySQL server via docker-compose.

(Following is taken from DataJoint documentation.)

• Create a directory to store the docker-compose YAML file:

mkdir mysql-docker
cd mysql-docker
wget https://raw.githubusercontent.com/datajoint/mysql-docker/master/docker-compose.yaml
docker-compose up -d

• Download a package that enables access to your locally running MySQL server:

Linux:

sudo apt-get install mysql-client

Mac (via Homebrew):

brew install mysql@5.7
brew tap homebrew/services
brew services start mysql@5.7
brew services list
brew link --force mysql@5.7
mysql -V # verify the installation

• Test the server access. If there are issues, refer here.

mysql -h 127.0.0.1 -u root -p
Enter password: [type in your password here: default is "simple"]

3. Install Epiphyte:

There are two ways to install epiphyte -- via pip or cloning this repo.

Note: certain features of the DataJoint python package have not been updated for more recent releases of Python. Therefore, DataJoint and epiphyte require an older version of Python (<=3.9). For this reason, we recommend using a conda environment to install all needed packages and to develop from.

Install via git

• Clone 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:

conda activate epiphyte

• Install the needed dependencies using setup.py:

pip install .

• Verify the installation:

conda list

Or, install via pip in a conda environment

• 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

Continue to Tutorial 4: Configure and connect to the database.