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SPARQL endpoint to represent pangenomic data

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oxiqle

oxiqle (OXIgraph-based pangenomic sparQL Endpoint) is a fork of oxigraph that includes rs-handlegraph. The purpose is to make pangenomic GFA-files accessible with SPARQL queries.

Oxigraph is a graph database implementing the SPARQL standard.

When cloning this codebase, don't forget to clone the submodules using git clone --recursive https://github.com/oxigraph/oxigraph.git to clone the repository including submodules or git submodule update --init to add the submodules to the already cloned repository.

Usage

Build oxi-handlegraph with:

cargo build --release

Run server:

./target/release/oxigraph_server serve -l <path_to_gfa>

Run query from CLI:

./target/release/oxigraph_server query -l <path_to_gfa> --results-file out.txt --query-file <path_to_sparql_query>

Help

Feel free to ask heringerp for help. Bug reports are also very welcome.

License

This project is licensed under either of

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in Oxigraph by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

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