bio-0.5.2: bio.cabal

Name:                bio
Version:             0.5.2
License:             LGPL
License-file:        LICENSE
Cabal-Version:       >= 1.6
Author:              Ketil Malde
Maintainer:          ketil@malde.org

Category:            Bioinformatics
Synopsis:            A bioinformatics library
Description:         This is a collection of data structures and algorithms
                     useful for building bioinformatics-related tools
                     and utilities.
                     .
                     Current list of features includes: a Sequence data type supporting
                     protein and nucleotide sequences and conversion between them.  As of version
                     0.4, different kinds of sequence have different types.  Support for quality
                     data, reading and writing Fasta formatted files, reading TwoBit and
                     phd formats, and Roche/454 SFF files.  Rudimentary (i.e. unoptimized) support
                     for doing alignments - including dynamic adjustment of scores based on sequence quality. 
                     Also Blast output parsing.  Partly implemented single linkage clustering, and
                     multiple alignment.  Reading Gene Ontology (GO) annotations (GOA) and
                     definitions\/hierarchy.
                     .
                     The Darcs repository is at: <http://malde.org/~ketil/biohaskell/biolib>.
Homepage:            http://biohaskell.org/Libraries/Bio

Tested-With:         GHC==6.12.1
Build-Type:          Simple
Data-Files:          README, Makefile

Flag test
  Description:       Build testing software
  Default:           False

Flag examples
  Description:       Build example programs
  Default:           True

Library
  Build-Depends:     base>=4 && <5, binary >=0.4 && <0.5, tagsoup>=0.8, bytestring >= 0.9.1,
                     containers, array, parallel, parsec, mtl, directory, QuickCheck >= 2

  Exposed-modules:   Bio.Sequence,
                     Bio.Sequence.SeqData,
                     Bio.Sequence.Fasta, Bio.Sequence.FastQ,
                     Bio.Sequence.TwoBit, Bio.Sequence.Phd,
                     Bio.Sequence.Entropy, Bio.Sequence.HashWord,
                     Bio.Sequence.GOA,
                     Bio.Sequence.GeneOntology,
                     Bio.Sequence.KEGG,
                     Bio.Sequence.AminoProperties,
                     Bio.Sequence.SFF, Bio.Sequence.SFF_name, Bio.Sequence.SFF_filters
                     Bio.Alignment.BlastData, Bio.Alignment.BlastFlat,
                     Bio.Alignment.Blast, Bio.Alignment.BlastXML,
                     Bio.Alignment.AlignData, Bio.Alignment.Matrices,
                     Bio.Alignment.SAlign, Bio.Alignment.AAlign, Bio.Alignment.QAlign
                     Bio.Alignment.Multiple, Bio.Alignment.ACE,
                     Bio.Alignment.Bowtie,
                     Bio.Alignment.Soap,
                     Bio.Alignment.BED, Bio.Alignment.PSL
                     Bio.Clustering,
                     Bio.Util, Bio.Util.Parsex
                     Bio.Location.Strand, Bio.Location.Position,
                     Bio.Location.ContigLocation, Bio.Location.Location, Bio.Location.LocMap,
                     Bio.Location.OnSeq, Bio.Location.SeqLocation, Bio.Location.SeqLocMap,
                     Bio.GFF3.Escape, Bio.GFF3.Feature, Bio.GFF3.FeatureHier, Bio.GFF3.FeatureHierSequences,
                     Bio.GFF3.SGD

  Extensions:        CPP, ParallelListComp
  if impl(ghc >= 6.12)
    Ghc-Options:       -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all -fno-warn-unused-do-bind
  else
    Ghc-Options:       -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all

Source-Repository head
  Type:           darcs
  Location:       http://malde.org/~ketil/biohaskell/biolib

Executable qc
  Main-Is:        Test.hs
  Other-Modules:  Bio.Util.TestBase, Bio.Util.Test,
                  Bio.Alignment.Test, Bio.GFF3.Test, Bio.Location.Test, Bio.Sequence.Test, Bio.Clustering.Test
  Hs-Source-Dirs: .  
  Build-Depends:  base >= 3 && <5, process, containers, random, QuickCheck >= 2, old-time
  if flag(test)
     Buildable:   True
  else
     Buildable:   False

-- Test.QuickBench needs to be ported to QC2.  Or everything moved over to criterion.
-- Executable qb
--  Main-Is:        Bench.hs
--  Other-Modules:  Test.QuickBench, Bio.Util.TestBase, Bio.Util.Test, 
--                  Bio.Alignment.Test, Bio.Sequence.Test, Bio.Clustering.Test
--  Hs-Source-Dirs: .  
--  Build-Depends:  base >= 3 && <5, process, containers, random

Executable flx
  Main-Is:        Flx.hs
  Hs-Source-Dirs: examples .
  Other-Modules:  Bio.Sequence.SFF
  Build-Depends:  base >= 3 && <5, bytestring
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable fastout
  Main-Is:        FastOut.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && <5  
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable     frecover
  Main-Is:        FRecover.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && < 5
  Ghc-Options:    -Wall
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable     frename
  Main-Is:        FRename.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && < 5, bytestring >= 0.9.1
  Ghc-Options:    -Wall
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable     flowclip
  Main-Is:        FlowClip.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && < 5
  Ghc-Options:    -Wall
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable     orf
  Main-Is:        Orf.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && < 5
  Ghc-Options:    -Wall
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False

Executable     rselect-pe
  Main-Is:        RSelectPE.hs
  Hs-Source-Dirs: examples .
  Build-Depends:  base >= 3 && < 5, random
  Ghc-Options:    -Wall
  if flag(examples)
     Buildable:   True
  else
     Buildable:   False