name:           RNAdesign
version:        0.1.2.2
author:         Christian Hoener zu Siederdissen
copyright:      Christian Hoener zu Siederdissen, 2013-2014
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 in
                the form of an IUPAC string. 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.
                .
                For more details please consult:
                <https://github.com/choener/RNAdesign/blob/master/README.md>
                .
                You can also run @RNAdesign --showmanual@ which will display
                the same @README.md@.
                .
                .
                .
                If you find this program useful, please cite:
                .
                @
                Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler
                Computational design of RNAs with complex energy landscapes
                2013. Biopolymers. 99, no. 12. 99. 1124–36.
                @
                .
                <http://dx.doi.org/10.1002/bip.22337>



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                >= 0.8.1            ,
    ParsecTools               >= 0.0.2 && < 0.0.3 ,
    PrimitiveArray            >= 0.5.3            ,
    RNAFold                   >= 1.99.3.3         ,
    ViennaRNA-bindings        >= 0.1.1.1
  exposed-modules:
    BioInf.RNAdesign
    BioInf.RNAdesign.Assignment
    BioInf.RNAdesign.CandidateChain
    BioInf.RNAdesign.Graph
    BioInf.RNAdesign.LogMultinomial
    BioInf.RNAdesign.OptParser
  ghc-options:
    -O2

executable RNAdesign
  build-depends:
    bytestring        >= 0.10   ,
    cmdargs           == 0.10.* ,
    file-embed        >= 0.0.6
  main-is:
    RNAdesign.hs
  ghc-options:
    -O2 -rtsopts