Re-implementation of gumpy in Rust for speed
cargo install grumpy
cargo add grumpy
pip install bio-grumpy
Running Rust unit tests
cargo test
Test coverage can be found with the use of tarpaulin.
# Install tarpaulin on first run
cargo install cargo-tarpaulin
# Generate an HTML coverage report
cargo tarpaulin --no-dead-code --engine llvm --out html
If you use grumpy in your work, please cite:
Westhead J, Baker CS, Brouard M, Colpus M, Constantinides B, Hall A, Knaggs J, Lopes Alves M, Spies R, Thai H, Surrall S, Govender K, Peto TEA, Crook DW, Omar SV, Turner R, Fowler PW
Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 Mycobacterium tuberculosis samples
Microbial Genomics 11:001592 doi:10.1099/mgen.0.001592
A BibTeX citation is included here