seqloc-datafiles-0.4: seqloc-datafiles.cabal

Name:                seqloc-datafiles
Version:             0.4
Cabal-Version:       >= 1.6
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

Flag Tests
  Description: Build test program
  Default:     False

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
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall

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 
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c

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 
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c

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
  Hs-Source-Dirs:      src, test
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c

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
  Hs-Source-Dirs:      src
  Ghc-options:         -Wall -rtsopts
  C-Sources:           src/rtsopts.c

Executable test-gtf
  if !flag(Tests)
     Buildable: False
  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

Executable test-bed
  if !flag(Tests)
     Buildable: False
  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
  Hs-Source-Dirs:      src, test
  Ghc-options:         -Wall

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