name:           RNAFold
version:        1.99.3.4
author:         Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al (ViennaRNA), 2010-2013
copyright:      Christian Hoener zu Siederdissen, 2010-2013
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:  >= 1.8.0
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.
                .
                Please use GHC 7.6 or newer.
                .
                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.

Extra-Source-Files:
  README.md

library
  build-depends:
    base            >=4&&<5     ,
    cmdargs         >= 0.10     ,
    containers                  ,
    deepseq         >= 1.3      ,
    lens            >= 3.8      ,
    primitive       >= 0.5      ,
    repa            >= 3.2      ,
    strict          >= 0.3.2    ,
    vector          >= 0.10     ,
    ADPfusion       >= 0.2.0.0  ,
    BiobaseTurner   >= 0.3.1.1  ,
    BiobaseVienna   >= 0.3      ,
    BiobaseXNA      >= 0.7      ,
    PrimitiveArray  >= 0.5
  exposed-modules:
    BioInf.ViennaRNA
    BioInf.ViennaRNA.Energy
    BioInf.ViennaRNA.Eval
    BioInf.ViennaRNA.Fold
    BioInf.ViennaRNA.Signature
  ghc-options:
    -Odph
    -funbox-strict-fields
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
    -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts

executable RNAFold
  build-depends:
    base >= 4 && < 5      ,
    cmdargs   >= 0.10     ,
    BiobaseTurner  >= 0.3 ,
    BiobaseVienna  >= 0.3 ,
    BiobaseXNA     >= 0.7 ,
    RNAFold
  main-is:
    RNAFold.hs
  hs-source-dirs:
    src
  ghc-options:
    -rtsopts
    -Odph
    -funbox-strict-fields
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
    -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts

executable RNAEval
  build-depends:
    base >= 4 && < 5      ,
    cmdargs   >= 0.10     ,
    BiobaseTurner  >= 0.3 ,
    BiobaseVienna  >= 0.3 ,
    BiobaseXNA     >= 0.7 ,
    RNAFold
  main-is:
    RNAEval.hs
  hs-source-dirs:
    src
  ghc-options:
    -rtsopts
    -Odph
    -funbox-strict-fields
    -funfolding-use-threshold100
    -funfolding-keeness-factor100
    -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts

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