grntools.cabal

Name:               grntools
Version:            0.2
Synopsis:           GRN tools for modeling from biological pathways.
Description:
  This program will convert a set of pathways written in a precise manner into 
  a discrete time, discrete space Markov chain, simulate its long run 
  probabilities, and transform those into an indication of how long each 
  protein is active for.
  .
  See the Paper "A Stochastic NF-kB Model Consistent with Pathway Information" 
  by Knight et al. for more information.
License:            BSD3
License-file:       LICENSE
Author:             Jason Knight <jason@jasonknight.us>
Maintainer:         Jason Knight <jason@jasonknight.us>
Build-Type:         Simple
Copyright:          2010, 2011, 2012 Jason Knight
Category:           Bioinformatics, Scientific Simulation, Simulation
Cabal-Version:	    >=1.8
Homepage:           http://www.jasonknight.us/software

Flag Library
  Description: Whether to build the library or not
  Default: False

Executable GrnSim
  Main-is:	        GrnSim.hs
  Build-Depends:    base >= 4,fgl,parsec,graphviz,containers,process,
                    regex-posix,directory,filepath,parseargs,Graphalyze,
                    random,statistics,gnuplot,vector,parallel,
                    deepseq,vector-strategies >0.1,pretty,text,
                    math-functions,mwc-random
  ghc-options:
        -rtsopts
        ---prof
        ---auto-all
        ---eventlog
        ---ddump-simpl-stats
        -with-rtsopts=-A16M
        -O -funbox-strict-fields
        -fno-spec-constr-count
        -threaded
  Extensions: FlexibleInstances

Library
  if flag(library)
    Build-Depends:    base >= 4,fgl,parsec,graphviz,containers,process,
                      regex-posix,directory,filepath,parseargs,Graphalyze,
                      random,statistics,gnuplot,vector,parallel,
                      deepseq,vector-strategies>0.1,pretty,text,
                      math-functions,mwc-random
  Else
    Buildable: False
  Exposed-Modules:  GRN.EM
                    GRN.Density
                    GRN.Render
                    GRN.Parse
                    GRN.Sparse
                    GRN.StateTransition
                    GRN.Types
                    GRN.Uncertainty
                    GRN.Utils
  Extensions: FlexibleInstances

Test-suite tests
  type:           exitcode-stdio-1.0
  hs-source-dirs: tests
  main-is:        tests.hs
  other-modules:
    Tests.Helpers
    Tests.Parse

  ghc-options:
    -threaded -rtsopts

  build-depends:
    grntools,
    containers,
    base,
    HUnit,
    QuickCheck >= 2,
    test-framework,
    test-framework-quickcheck2,
    test-framework-hunit,
    math-functions