seqloc-datafiles-0.4.2: seqloc-datafiles.cabal

Name:                seqloc-datafiles
Version:             0.4.2
Cabal-Version:       >= 1.10
Synopsis:            Read and write BED and GTF format genome annotations
Description:         Read and write BED and GTF format genome annotations
License:             MIT
License-File:        LICENSE
Author:              Nick Ingolia
Maintainer:          nick@ingolia.org
Build-Type:          Simple
Category:            Bioinformatics
Homepage:            http://www.ingolia-lab.org/seqloc-datafiles-tutorial.html

Source-Repository head
  type: git
  location: http://github.com/ingolia/seqloc
  subdir: seqloc-datafiles

Library
  Exposed-modules:     Bio.SeqLoc.Bed, Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable
  Other-modules:       Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       lifted-base >= 0.2.3, transformers-base >= 0.4.3,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,
                       conduit, conduit-extra, resourcet
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall
  Default-Language:    Haskell2010

Executable gtf-to-bed
  Main-is:             GtfToBed.hs
  Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.Bed, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2, transformers, monads-tf,
                       lifted-base, transformers-base, conduit, conduit-extra, resourcet
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c
  Default-Language:    Haskell2010

Executable bed-to-gtf
  Main-is:             BedToGtf.hs
  Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.Bed, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2, transformers, monads-tf,
                       conduit, conduit-extra, lifted-base, transformers-base, resourcet
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c
  Default-Language:    Haskell2010

Executable gtf-introns
  Main-is:             GtfIntrons.hs
  Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,
                       QuickCheck, random, cmdtheline,
                       conduit, conduit-extra, resourcet
  Hs-Source-Dirs:      src, test
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c
  Default-Language:    Haskell2010

Executable bed-subregion
  Main-is:             BedSubregion.hs
  Other-modules:       Bio.SeqLoc.Bed, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2, transformers, monads-tf,
                       pretty, conduit, conduit-extra, resourcet, cmdtheline, filepath, lifted-base,
                       transformers-base, resourcet
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c
  Default-Language:    Haskell2010

Executable genome-to-trx
  Main-is:             GenomeToTrx.hs
  Buildable:           False
  Other-modules:       Bio.SeqLoc.Bed
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.6, biocore >= 0.2,
                       conduit, conduit-extra, vector, filepath, resourcet
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall
  Default-Language:    Haskell2010

Test-suite test-gtf
  Type:                exitcode-stdio-1.0
  Main-is:             TestGtf.hs
  Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,
                       QuickCheck, random
  Hs-Source-Dirs:      src, test
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c
  Default-Language:    Haskell2010

Test-Suite test-bed
  Type:                exitcode-stdio-1.0
  Main-is:             TestBed.hs
  Other-modules:       Bio.SeqLoc.Bed, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils
  Build-depends:       base >= 4.2 && < 5, bytestring,
                       attoparsec >= 0.8.5, hashable, unordered-containers,
                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,
                       QuickCheck, random, lifted-base, transformers-base,
                       conduit, conduit-extra
  Hs-Source-Dirs:      src, test
  Ghc-options:         -Wall
  Default-Language:    Haskell2010

Test-Suite test-subregions
  Type: exitcode-stdio-1.0
  Main-is:             TestSubregions.hs
  Other-modules:       Bio.SeqLoc.Bed
  Build-depends:       base >= 4.2 && < 5, bytestring, attoparsec >= 0.8.5,
                       QuickCheck, random, biocore >= 0.2, unordered-containers, vector, hashable,
                       seqloc >= 0.5, lifted-base, transformers-base, conduit, conduit-extra,
                       iteratee, directory, process, transformers
  Hs-Source-Dirs:      src, test
  Default-Language:    Haskell2010