name:           Nussinov78
version:        0.0.1.1
author:         Christian Hoener zu Siederdissen, 2011-2012
copyright:      Christian Hoener zu Siederdissen, 2011-2012
homepage:       http://www.tbi.univie.ac.at/~choener/adpfusion
maintainer:     choener@tbi.univie.ac.at
category:       Bioinformatics
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.6.0
synopsis:
                Nussinov78 using the ADPfusion library.
description:
                The Nussinov78 RNA secondary structure prediction algorithm
                using the ADPfusion framework.
                .
                This algorithm is simple enough to be used as a tutorial-type
                example. It also shows that efficient code is possible. The
                ADPfusion code compared to C is slower by a factor of only 1.8.
                We plan to improve upon this.
                .
                A number of helper functions currently present in
                BioInf.Nussinov78 will later move in their own library.
                .
                If possible, build using the GHC llvm backend, and GHC-7.2.2.
                GHC-7.4.x produces very bad code on my system, please benchmark
                using 7.2.2.
                .
                For comparison, a version of the algorithm written in C is
                available under C/nussinov.c. Use at least
                "gcc -O3 nussinov.c".

Extra-Source-Files:
  C/nussinov.c

Flag llvm
  description: build using llvm backend
  default: True



library
  build-depends:
    base >= 4 && < 5,
    mtl            >= 2,
    primitive      == 0.4.*   ,
    vector         == 0.9.*   ,
    PrimitiveArray == 0.2.1.1 ,
    BiobaseXNA     == 0.6.2.4 ,
    ADPfusion      == 0.0.1.0
  exposed-modules:
    BioInf.Nussinov78
  ghc-options:
    -Odph
    -funbox-strict-fields
    -fspec-constr
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
  if flag (llvm)
    ghc-options:
      -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts



executable Nussinov78
  build-depends:
--    base >= 4 && < 5,
--    mtl,
--    primitive      == 0.4.*   ,
--    vector         == 0.9.*   ,
--    PrimitiveArray == 0.2.1.1 ,
--    BiobaseXNA     == 0.6.2.2 ,
--    ADPfusion      == 0.0.1.0
  main-is:
    Nussinov78.hs
  other-modules:
    BioInf.Nussinov78
  ghc-options:
    -rtsopts
    -Odph
    -funbox-strict-fields
    -fspec-constr
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
  if flag (llvm)
    ghc-options:
      -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts



source-repository head
  type: git
  location: git://github.com/choener/Nussinov78