name:           RNAFoldProgs
version:        0.0.0.3
author:         Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al. (ViennaRNA package)
maintainer:     choener@tbi.univie.ac.at
copyright:      Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al. (ViennaRNA package)
category:       Bioinformatics
synopsis:       RNA secondary structure folding
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.4.0
description:
                RNA secondary structure following "Fast Folding and Comparison
                of RNA Secondary Structures, Hofacker et al., 1994". Uses the
                Turner 2004 parameter set. The algorithm work on an algebraic
                ring structure that is instanciated as required. This
                prelimenary release contains the minimum-free energy version
                only.
                .
                - Do not expect good runtimes with anything less than
                  6.13.201008xx. The newest head produces an executable roughly
                  20x faster than GHC 6.12.3.
                .
                - Bugs are likely present in this algorithm. If you find one,
                  please send me a mail.
                .
                - One goal is to get the vector library to optimise the loops
                  (fold's) in such a way as to get performance close to the
                  ViennaRNA package. Right now, we are about 15x slower.
                .
                - Works well with -Odph, -fllvm (llvm is about 70% faster than
                  -fasm)
                .
                - 0.0.0.3 forgot a lot of depends!

executable hsRNAFold
  build-depends:
    base >=4 && <5,
    containers,

    cmdargs ==0.6,
    primitive >=0.3 && <0.4,
    vector >=0.7 && <0.8,

    HsTools >=0.0.1.1,
    Biobase >=0.0.2 && <0.0.3,
    BiobaseTypes >=0.0.2.1 && <0.0.3,
    BiobaseTurner >=0.0.2.1 && <0.0.3,
    BiobaseVienna >=0.0.2 && <0.0.3,
    PrimitiveArray >=0.0.2 && <0.0.3,
    RNAFold >=0.0.2 && <0.0.3

  main-is:
    RNAFold.hs

  ghc-options:
    -Odph
    -fno-method-sharing

executable hsRNAEval
  build-depends:
    base >=4 && <5,

    cmdargs ==0.6,
    split >=0.0.2.1,

    Biobase >=0.0.2 && <0.0.3,
    RNAFold >=0.0.2 && <0.0.3

  main-is:
    RNAEval.hs

  ghc-options:
    -Odph