name:                bioinformatics-toolkit
version:             0.9.0
synopsis:            A collection of bioinformatics tools
description:         A collection of bioinformatics tools
license:             MIT
license-file:        LICENSE
author:              Kai Zhang
maintainer:          kai@kzhang.org
copyright:           (c) 2014-2019 Kai Zhang
category:            Bio
build-type:          Simple
extra-source-files:  README.md
cabal-version:       >=1.18
data-files:
  tests/data/example.bam
  tests/data/example.bed
  tests/data/pairedend.bam
  tests/data/pairedend.bedpe
  tests/data/peaks.bed
  tests/data/peaks.sorted.bed
  tests/data/example_intersect_peaks.bed
  tests/data/motifs.fasta
  tests/data/motifs.meme
  tests/data/test.fastq

library
  hs-source-dirs: src
  ghc-options: -Wall

  exposed-modules:
    Bio.ChIPSeq.FragLen
    Bio.Data.Bed
    Bio.Data.Bed.Types
    Bio.Data.Bed.Utils
    Bio.Data.Bam
    Bio.Data.Fasta
    Bio.Data.Fastq
    Bio.GO
    Bio.GO.Parser
    Bio.Motif
    Bio.Motif.Alignment
    Bio.Motif.Merge
    Bio.Motif.Search
    Bio.RealWorld.BioGRID
    Bio.RealWorld.ENCODE
    Bio.RealWorld.Ensembl
    Bio.RealWorld.GENCODE
    Bio.RealWorld.GDC
    Bio.RealWorld.ID
    Bio.RealWorld.Reactome
    Bio.RealWorld.UCSC
    Bio.RealWorld.Uniprot
    Bio.Seq
    Bio.Seq.IO
    Bio.Utils.BitVector
    Bio.Utils.Functions
    Bio.Utils.Misc
    Bio.Utils.Overlap
    Bio.Utils.Types

  build-depends:
      base >=4.11 && <5.0
    , aeson
    , aeson-pretty
    , attoparsec
    , bytestring >= 0.10
    , bytestring-lexing >= 0.5
    , case-insensitive
    , clustering
    , conduit >= 1.3.0
    , conduit-extra
    , containers >= 0.5
    , data-ordlist
    , data-default-class
    , double-conversion
    , HsHTSLib >= 1.9.2
    , http-conduit >= 2.1.8
    , hexpat
    , IntervalMap >= 0.5.0.0
    , microlens
    , microlens-th
    , matrices >= 0.5.0
    , mtl >= 2.1.3.1
    , math-functions
    , parallel >= 3.2
    , primitive
    , split
    , statistics >= 0.13.2.1
    , text >= 0.11
    , transformers >= 0.3.0.0
    , unordered-containers >= 0.2
    , word8
    , vector
    , vector-algorithms

  default-language:    Haskell2010

benchmark bench
  type: exitcode-stdio-1.0
  main-is: benchmarks/bench.hs
  default-language:    Haskell2010
  build-depends:
      base >=4.8 && <5.0
    , bioinformatics-toolkit
    , random
    , criterion
    , clustering
    , bytestring
    , data-default-class
    , conduit
    , mtl

test-suite tests
  type: exitcode-stdio-1.0
  hs-source-dirs: tests
  main-is: test.hs
  other-modules:
      Tests.Bed
    , Tests.Bam
    , Tests.Fastq
    , Tests.Motif
    , Tests.Seq
    , Tests.Tools

  default-language:    Haskell2010
  build-depends:
      base
    , bytestring
    , random
    , vector
    , data-default-class
    , microlens
    , tasty
    , tasty-golden
    , tasty-hunit
    , bioinformatics-toolkit
    , conduit
    , conduit-combinators
    , unordered-containers
    , mtl
    , matrices

source-repository  head
  type: git
  location: https://github.com/kaizhang/bioinformatics-toolkit.git