name:           RNAdesign
version:        0.0.2.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@tbi.univie.ac.at
category:       Bioinformatics
synopsis:       Multi-target RNA sequence design
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.6.0
description:
                The RNA sequence design problem asks for a single sequence that
                readily folds into the one or more structural targets that are
                given as input.
                .
                This program expects on standard input a file with one or more
                structures and, possibly, additional sequence constraints. It
                will then run a Markov chain to find a sequence that is optimal
                with regard to the structural targets and the user-defineable
                optimization function.
                .
                The user can give different optimization criteria on the
                command line, akin to a simple calculator.
                .
                .
                .
                If you find this program useful, please cite:
                .
                Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler
                .
                @A Graph Coloring Approach to Designing Multi-Stable Nucleic Acid Sequences@
                .
                Biopolymers, 99, 12, 1124-1136, 2013, Wiley



extra-source-files:
  changelog
  README.md

library
  build-depends:
    base              >= 4 && < 5 ,
    array             >= 0.4  ,
    containers                ,
    fgl               >= 5.4  ,
    lens              >= 3.9  ,
    monad-primitive   >= 0.1  ,
    mwc-random-monad  >= 0.6  ,
    parallel          >= 3.2  ,
    parsec            >= 3    ,
    primitive         >= 0.5  ,
    random            >= 1.0  ,
    transformers      >= 0.3  ,
    tuple             >= 0.2  ,
    vector            >= 0.10 ,
    fgl-extras-decompositions >= 0.1.0.0          ,
    BiobaseTurner             >= 0.3.1.1          ,
    BiobaseVienna             >= 0.3              ,
    BiobaseXNA                >= 0.7.0.1          ,
    ParsecTools               >= 0.0.2 && < 0.0.3 ,
    PrimitiveArray            >= 0.5              ,
    RNAFold                   >= 1.99.3.3         ,
    ViennaRNA-bindings        >= 0.0.2.3
  exposed-modules:
    BioInf.RNAdesign
    BioInf.RNAdesign.Assignment
    BioInf.RNAdesign.Graph
    BioInf.RNAdesign.LogMultinomial
    BioInf.RNAdesign.OptParser
  ghc-options:
    -O2

executable RNAdesign
  build-depends:
    base              >= 4 && < 5 ,
    array             >= 0.4      ,
    cmdargs           == 0.10.*   ,
    containers                    ,
    fgl               >= 5.4      ,
    lens              >= 3.9      ,
    monad-primitive   >= 0.1      ,
    mwc-random-monad  >= 0.6      ,
    parallel          >= 3.2      ,
    parsec            >= 3        ,
    primitive         >= 0.5      ,
    random            >= 1.0      ,
    transformers      >= 0.3      ,
    tuple             >= 0.2      ,
    vector            >= 0.10     ,
    fgl-extras-decompositions >= 0.1.0.0          ,
    BiobaseTurner             >= 0.3.1.1          ,
    BiobaseVienna             >= 0.3              ,
    BiobaseXNA                >= 0.7.0.1          ,
    ParsecTools               >= 0.0.2 && < 0.0.3 ,
    PrimitiveArray            >= 0.5              ,
    RNAFold                   >= 1.99.3.3         ,
    ViennaRNA-bindings        >= 0.0.2.3
  main-is:
    RNAdesign.hs
  ghc-options:
    -O2 -rtsopts