This repository provides a convenient way to build the current setup of "GenussFold" for RNA pseudoknot grammars.

There are two options on how to build this project. Both provide a full build environment. Building via nix has the advantage of providing a known-good set of ghc, llvm, and all dependencies (even standard C libraries).

Run cabal build exe:GenussFold in the top-level directory.

Run a test like so: zcat ADPfusion/runtimes/0100.input.gz | head -n 1 | head -c 50 | dist-newstyle/build/x86_64-linux/ghc-9.0.2/GenussFold-0.0.0.3/x/GenussFold/build/GenussFold/GenussFold +RTS -s -RTS

• An input of 50 nucleotides (from the set of testing sequences)
• with activated @+RTS -s@ runtime information, which will print the running time

If you have nix installed with flakes, then call in the top-level directory: nix develop

Once you are in a shell, you can build the project thusly: buildcabal GenussFold/src/GenussFold.hs

an then run the same test as above: zcat ADPfusion/runtimes/0100.input.gz | head -n 1 | head -c 50 | ./GenussFold/src/GenussFold +RTS -s -RTS