glama: Genomic long-read analysis modules and applications.
Documentation for the API can be found on the documentation page.
Glama 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).
pip is recommended for installation.
pip install glama
To build from source (particularly for those interested in contributing to the code), follow the procedure below.
# Clone repository.
git clone https://github.com/broadinstitute/glama.git
cd glama
# Create a Python virtual environment and install Maturin, the tool that
# will compile the Rust and Python code into a complete library.
# For more information on Maturin, visit https://github.com/PyO3/maturin .
python -mvenv venv
. venv/bin/activate
pip install maturin
# Build the library (with release optimizations) and install it in
# the currently active virtual environment.
maturin develop --releaseglama is compiled for Linux and MacOSX. Windows is not currently supported.
If you encounter bugs or have questions/comments/concerns, please file an issue on our Github page.
For information on contributing to glama development, visit our developer documentation.