name:           RNAFold
version:        1.99.1.3
author:         Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al (ViennaRNA), 2010-2012
copyright:      Christian Hoener zu Siederdissen, 2010-2012
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:       RNA secondary structure prediction
description:
                RNAfold v2 using the ADPfusion library. The RNAfold algorithm
                is used to determine how fast we can be compared to a highly
                optimized C program.
                .
                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.
                .
                NOTE I'd like to rename this package to RNAfold, like the C
                implementation. Do not install "globally", especially if you
                normally use RNAfold from the ViennaRNA package, for obvious
                reasons.
                .
                NOTE I am reluctant to call this v2 for now.

Extra-Source-Files:
  BioInf/RNAfold/QuickCheck.hs
  README.md

Flag llvm
  description: build using llvm backend
  default: True



library
  build-depends:
    base >= 4 && < 5,
    mtl            >= 2,
    strict         >= 0.3.2,
    primitive      == 0.4.*   ,
    vector         == 0.9.*   ,
    PrimitiveArray == 0.2.2.0 ,
    BiobaseVienna  == 0.2.2.5 ,
    BiobaseXNA     == 0.6.2.5 ,
    ADPfusion      == 0.0.1.2
  exposed-modules:
    BioInf.RNAfold
    BioInf.RNAfold.Combinators
    BioInf.RNAfold.Energy
    BioInf.RNAfold.Library
  ghc-options:
    -O2
    -funbox-strict-fields
    -fspec-constr
    -fspec-constr-threshold=500
    -fspec-constr-count=10
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
    -fsimplifier-phases10
  if flag (llvm)
    ghc-options:
      -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts



executable RNAFold
  build-depends:
--    we get all build depends from the library dependencies
  main-is:
    RNAFold.hs
  other-modules:
    BioInf.RNAfold
    BioInf.RNAfold.Combinators
    BioInf.RNAfold.Energy
    BioInf.RNAfold.Library
  ghc-options:
    -rtsopts
    -O2
    -funbox-strict-fields
    -fspec-constr
    -fspec-constr-threshold=500
    -fspec-constr-count=10
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
    -fsimplifier-phases10
  if flag (llvm)
    ghc-options:
      -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts



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