README.rst

hidive

Hidive is a targeted genome co-assembler for biobank-scale long-read and short-read data.

Documentation for the API can be found on the documentation page.

Quick start

The following commands will compile the Rust and Python codebase.

# Install Rust.
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Download and build Hidive
git clone https://github.com/broadinstitute/hidive.git
cd hidive
cargo build --release

# Configure Python environment
python -mvenv venv
. venv/bin/activate
pip install -f dev-requirements.txt

# Build Hidive's Python codebase, Pydive.
cd src/pydive/
maturin develop --release

Prerequisites

Hidive is designed to access local files or data in Google Cloud Storage (GCS). Within certain cloud-computing environments (i.e. Terra, All of Us Researcher Workbench), access to GCS is already configured. For accessing files in GCS on your local machine, you will also need to install the Google Cloud CLI. Then, configure your Application Default Credentials (ADC).

If accessing requester pays buckets , set the following environment variable before running hidive commands:

export GCS_REQUESTER_PAYS_PROJECT=<Google Project ID>

Installation

At the moment, Hidive is under active development and is not yet available through standard bioinformatic software channels (pip, conda, cargo, etc.).

Building from source

To build the primary Rust source, follow the procedure below.

To optionally build the Python bindings to the Rust codebase, follow the procedure below after performing the above steps.

Supported platforms

Hidive is compiled for Linux and MacOSX. Windows is not currently supported.

Getting help

If you encounter bugs or have questions/comments/concerns, please file an issue on our Github page.

Developers' guide

For information on contributing to Hidive development, visit our developer documentation.