homology-explorer

A tool for exploring orthology and paralogy relationships in model organism species.

Demonstration Video

Requirements

Software

• node v18.16.0+ (https://nodejs.org)
• pnpm v8.3.1+ (https://pnpm.io/)
• python v3.10 (https://python.org)
• poetry v1.4.2+ (https://python-poetry.org/)

Note: This repository uses pnpm to manage javascript dependencies. Using npm or yarn may cause issues due to the lock files not being used.

Data

The homology-explorer has only been tested to work with DIOPT v8.5 TSV files. The following files need to be obtained from DIOPT in order for the visualization to work. Place these files (uncompressed) in the data directory.

• Gene_Information.tsv
• Ortholog_Pair_Best.tsv

Optional

Only required for Markdown to PDF conversion

• pandoc
• tex

Getting Started

The following commands clone the repo and install the javascript and python dependencies.

git clone [email protected]:jogoodma/homology-explorer.git
cd homology-explorer
pnpm install
poetry install

Development

Script commands

Formatting

black is used for formatting python code. The configuration options for black are controlled via the [tool.black] section of the pyproject.toml file.

prettier is used for formatting JavaScript, Typescript, and Markdown files

Setup

1. Follow the steps under [Getting Started](#Getting Started).
2. Install the pre-commit hooks.

poetry run pre-commit install

PDF Generation

This package uses pandoc, tex, and mermaid-filter to generate PDF documentation from markdown files. To generate a PDF first install pandoc and tex via your OS installer of choice then do the following.

1. Clone the repo (if you have not already)
2. Change to repo directory
3. Install mermaid-filter
4. Run the command to generate a PDF

git clone [email protected]:jogoodma/homology-explorer.git
cd homology-explorer
pnpm install
pnpm run [DOCUMENT SCRIPT TARGET]

Replace [DOCUMENT SCRIPT TARGET] with one of the available commands listed under scripts in the package.json file.

e.g.

pnpm run pandoc:proposal

Docker

Requirements:

• Docker
• Docker compose
• DIOPT data files (in the data directory):
  • Gene_Information.tsv
  • Ortholog_Pair_Best.tsv
  • Species.tsv

To run a production build in Docker use the following commands.

docker volume create he_caddy_data
docker compose up -d --build

The volume command is only required one time. This will build the database, the API server, the UI, and start a production server on port 8000. To change the port set the HOMOLOGY_EXPLORER_PORT environment variable.

e.g.

echo "HOMOLOGY_EXPLORER_PORT=8888" >> .env

Docker container overview

flowchart LR
    user(User) == "port 8000" ==> proxy(Caddy Server)
    subgraph docker[Docker]
        proxy == "/api/* on port 80" ==> api(FastAPI)
        proxy == "port 4173" ==> UI(React App)
        subgraph d1[Proxy service]
            proxy
        end
        subgraph d2[UI service]
            UI
        end
        subgraph d3[API service]
            api ==> database[(DuckDB)]
        end
    end

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