atlas

atlas provides tools for gene expression analyses.

It is split into a command-line application and server.

CLI

The CLI includes commands to perform gene expression quantification (quantify), normalize counts (normalize), and cluster raw counts using t-SNE (transform).

Prerequisites

• Rust

Build

$ cargo build --release --package atlas-cli

By default, the binary is written to target/release/atlas.

Run

See atlas --help for more information.

Server

The server includes a REST API over HTTP. It is an optional component that can be used to store quantifications in an associated database.

Prerequisites

• Rust
• PostgreSQL
• sqlx-cli (cargo install sqlx-cli --no-default-features --features native-tls,postgres)

Build

$ cargo build --release --package atlas-server

By default, the binary is written to target/release/atlas-server.

Run

$ sqlx database setup --source atlas-server/migrations
$ atlas-server

OpenAPI documentation can then be viewed at http://<local-address>/docs.

Development quickstart

atlas defines a development container manifest to quickly build an environment for development and testing. This is compatible with, e.g., GitHub Codespaces and Visual Studio Code with the Dev Containers extension installed.

For server development,

cp .env.example .env
sqlx database setup --source atlas-server/migrations
cargo run -- server

# open <local-address>/docs

Legal

This project is licensed as either Apache 2.0 or MIT at your discretion. Additionally, please see the disclaimer that applies to all crates and command line tools made available by St. Jude Rust Labs.