This documents is incomplete.
This document is intended to help you in getting the genome browser setup and running on your local machine for debugging and development purposes.
Python is an interpreted, high-level and general-purpose programming language. Python's design philosophy emphasizes code readability with its notable use of significant indentation.
Installation guide: https://www.python.org/downloads/
Please note that you might need to install the required python packages using the command python3 rather than python if you also have Python 2 installed.
pip is the package installer for Python.
Installation guide: https://pip.pypa.io/en/stable/installing/
rustc is the compiler for the Rust programming language, provided by the project itself. Compilers take your source code and produce binary code, either as a library or executable.
Installation guide: https://www.rust-lang.org/tools/install
More info: https://doc.rust-lang.org/rustc/what-is-rustc.html
Cargo is the Rust package manager. Cargo downloads your Rust package's dependencies, compiles your packages, makes distributable packages, and uploads them to crates.io, the Rust community’s package registry.
Cargo usually gets shipped along with rustc so we may not have to install it separately.
Uvicorn is a lightning-fast ASGI server implementation, using uvloop and httptools.
Installation guide and more info: https://www.uvicorn.org/
wasm-pack helps you build rust-generated WebAssembly packages that you could publish to the npm registry, or otherwise use alongside any javascript packages in workflows that you already use, such as webpack.
Installation guide: https://rustwasm.github.io/wasm-pack/installer/
More: https://github.com/rustwasm/wasm-pack
FastAPI is a modern, fast (high-performance), web framework for building APIs with Python 3.6+ based on standard Python type hints.
Installation command: $ pip install fastapi
More info: https://pypi.org/project/fastapi/
Loguru is a library which aims to bring enjoyable logging in Python.
Installation command: $ pip install loguru
More info: https://pypi.org/project/loguru/
YAML is a data serialization format designed for human readability and interaction with scripting languages. PyYAML is a YAML parser and emitter for Python.
Installation guide: $ pip install pyyaml
A Python library for parsing and creating TOML.
Installation guide: $ pip install toml
This library provides encoding and decoding for the Concise Binary Object Representation (CBOR) (RFC 7049) serialization format.
Installation command: $ pip install cbor2
More info: https://cbor2.readthedocs.io/en/latest/
A package for accessing bigWig files using libBigWig
Installation command: $ pip install pyBigWig
HTTP library for Python.
Installation command: $ pip install requests
The path is configured in core/config.py in a variable called DATA_FILES where it's pulled in from .env
INTERNAL ONLY
Download an unpack the following file inside the data files directory (./example-data/data/) before starting the backend server:
/homes/dan/datafile-upload.tar.gz
Copy from ebi-cli-001:
$ rsync -aWv your-username@noah-login-01:/homes/dan/datafile-upload.tar.gz backend-server/example_data/data/
Unpack by running:
$ tar -xf datafile-upload.tar.gz
Starting the backend server:
$ ./build.sh
The standalone application can be started by running the following:
$ cargo build
$ ./build.sh
The server will be started and run on port 8000 on your local machine.
The port can be changed by updating it in the file ./build.sh