BiobaseXNA-0.9.2.1: BiobaseXNA.cabal

name:           BiobaseXNA
version:        0.9.2.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       https://github.com/choener/BiobaseXNA
bug-reports:    https://github.com/choener/BiobaseXNA/issues
copyright:      Christian Hoener zu Siederdissen, 2011 - 2015
category:       Bioinformatics
synopsis:       Efficient RNA/DNA representations
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
tested-with:    GHC == 7.8.4, GHC == 7.10.1
cabal-version:  >= 1.10.0
description:
                This is a base library for bioinformatics with emphasis on RNA
                and DNA primary structure as well as amino acid sequences.
                .
                Provided are efficient encodings for short sequences, as
                required by RNA folding tools. Extended RNA secondary
                structures can be represented as well.
                .
                Contains data from:
                .
                @
                Frequency and isostericity of RNA base pairs
                Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis
                Nucl. Acids Res. (2009)
                @
                .
                <http://dx.crossref.org/10.1093%2Fnar%2Fgkp011>



extra-source-files:
  sources/isostericity-matrices.csv
  sources/isostericity-detailed.csv
  sources/iupac-nucleotides
  sources/codontable
  changelog.md
  README.md

data-files:
  sources/iupac-nucleotides



library
  build-depends: base                     >= 4.7      && < 4.9
               , aeson                    >= 0.8      && < 0.11
               , bimaps                   >= 0.0.0.2  && < 0.0.1.0
               , binary                   >= 0.7      && < 0.8
               , bytes                    >= 0.15     && < 0.16
               , bytestring               >= 0.10     && < 0.11
               , cereal                   >= 0.4      && < 0.5
               , cereal-vector            >= 0.2      && < 0.3
               , containers               >= 0.5      && < 0.6
               , csv                      >= 0.1      && < 0.2
               , deepseq                  >= 1.3      && < 1.5
               , file-embed               >= 0.0.8    && < 0.0.10
               , hashable                 >= 1.2      && < 1.3
               , lens                     >= 4.0      && < 4.14
               , primitive                >= 0.5      && < 0.7
               , PrimitiveArray           >= 0.7.0    && < 0.7.1
               , split                    >= 0.2      && < 0.3
               , text                     >= 1.0      && < 1.3
               , tuple                    >= 0.3      && < 0.4
               , vector                   >= 0.10     && < 0.12
               , vector-binary-instances  >= 0.2      && < 0.3
               , vector-th-unbox          >= 0.2      && < 0.3
  exposed-modules:
    Biobase.Primary
    Biobase.Primary.AA
    Biobase.Primary.Bounds
    Biobase.Primary.Hashed
    Biobase.Primary.IUPAC
    Biobase.Primary.Letter
    Biobase.Primary.Nuc
    Biobase.Primary.Nuc.Conversion
    Biobase.Primary.Nuc.DNA
    Biobase.Primary.Nuc.RNA
    Biobase.Primary.Nuc.XNA
    Biobase.Primary.Trans
    Biobase.Primary.Unknown
    Biobase.Secondary
    Biobase.Secondary.Basepair
    Biobase.Secondary.Constraint
    Biobase.Secondary.Diagrams
    Biobase.Secondary.Isostericity
    Biobase.Secondary.Pseudoknots
    Biobase.Secondary.Structure
    Biobase.Secondary.Vienna
  default-extensions: BangPatterns
                    , DeriveGeneric
                    , EmptyDataDecls
                    , FlexibleContexts
                    , FlexibleInstances
                    , GeneralizedNewtypeDeriving
                    , LambdaCase
                    , MultiParamTypeClasses
                    , PatternSynonyms
                    , ScopedTypeVariables
                    , TemplateHaskell
                    , TypeFamilies
                    , TypeOperators
                    , UndecidableInstances
                    , ViewPatterns
  default-language:
    Haskell2010
  ghc-options:
    -O2 -funbox-strict-fields



executable SubOptDistance
  build-depends: base
               , BiobaseXNA
               , cmdargs      >= 0.10   && < 0.11
  main-is:
    SubOptDistance.hs
  hs-source-dirs:
    src
  default-language:
    Haskell2010
  default-extensions: DeriveDataTypeable
                    , NoMonomorphismRestriction
                    , RecordWildCards
                    , ScopedTypeVariables
  ghc-options:
    -O2



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