name:                RNAlien
version:             1.3.1
synopsis:            Unsupervized construction of RNA family models
description:         RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
                     .
                     It is available as a commandline tool, for testing or construction of few sequences the webservice can be used.
                     .
                     The source code of RNAlien, as well as the webserver is open source and available via GitHub (License GPL-3):
		     .
		     * <https://github.com/eggzilla/RNAlien RNAlien>
		     .
		     * <https://github.com/eggzilla/AlienServer AlienServer>
                     .
                     TaxonomyTools which can be used to visualise the organisms included in a RNAlien result can be found here (License GPL-3):
		     .
		     * <https://github.com/eggzilla/TaxonomyTools TaxonomyTools-Github>
		     .
		     * <https://hackage.haskell.org/package/Taxonomy TaxonomyTools-Hackage>
                     .
                     For instruction how to use RNAlien please see the <http://rna.tbi.univie.ac.at/rnalien/help Help page>.
                     .
                     Dependencies:
		     .
                     * <http://infernal.janelia.org/ Infernal>
		     .
		     * <http://www.bioinf.uni-freiburg.de/Software/LocARNA/#download Locarna>
		     .
		     * <https://www.tbi.univie.ac.at/~wash/RNAz/ RNAz>
                     .
                     * <http://wash.github.io/rnacode/ RNAcode>                        
		     .
		     * <http://www.tbi.univie.ac.at/RNA/index.html#download ViennaRNA package>
                     .
                     Installation via cabal-install:
                     .
                     > cabal install RNAlien
		     
license:             GPL-3
license-file:        LICENSE
author:              Florian Eggenhofer
maintainer:          egg@tbi.univie.ac.at
-- copyright:           
category:            Bioinformatics
build-type:          Simple
cabal-version:       >=1.8

source-repository head
  type:     git
  location: https://github.com/eggzilla/RNAlien

source-repository this
  type:     git
  location: https://github.com/eggzilla/RNAlien/tree/1.3.1
  tag:      1.3.1
                     
executable RNAlien
  Hs-Source-Dirs:      ./src/Bio/
  main-is:	       RNAlien.hs   
  ghc-options:         -Wall -O2
  build-depends:       base >=4.5 && <5, cmdargs, directory, biofasta, random, biocore, containers, RNAlien, time, either-unwrap, filepath

executable RNAlienStatistics
  Hs-Source-Dirs:      ./src/Bio/
  main-is:             RNAlienStatistics.hs
  ghc-options:         -Wall -O2
  build-depends:       base >=4.5 && <5, cmdargs, cassava, vector, process, bytestring, either-unwrap, RNAlien, directory, biofasta, biocore, split, filepath, ViennaRNAParser>=1.3.2

executable SelectSequences
  Hs-Source-Dirs:      ./src/Bio/
  main-is:             SelectSequences.hs
  ghc-options:         -Wall -O2
  build-depends:       base >=4.5 && <5, cmdargs, either-unwrap, RNAlien

executable cmsearchToBed
  Hs-Source-Dirs:      ./src/Bio/
  main-is:             cmsearchToBED.hs
  ghc-options:         -Wall -O2
  build-depends:       base >=4.5 && <5, cmdargs, either-unwrap, RNAlien, bytestring, text

executable RNAcentralHTTPRequest
  Hs-Source-Dirs:      ./src/Bio/
  main-is:             RNAcentralHTTPRequest.hs
  ghc-options:         -Wall -O2
  build-depends:       base >=4.5 && <5, cmdargs, either-unwrap, RNAlien
  
Library
  Hs-Source-Dirs:      ./src/
  ghc-options:         -Wall -O2 -fno-warn-unused-do-bind
  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory, blastxml>=0.3.2, biofasta, parsec, random, BlastHTTP>=1.2.1, biocore, bytestring, Taxonomy >= 1.0.2, either-unwrap, containers, ClustalParser>=1.2.1, EntrezHTTP>=1.0.3, vector, edit-distance, cassava, matrix, hierarchical-clustering, filepath, HTTP, http-conduit, hxt, network, aeson, text, transformers, pureMD5, http-types, text-metrics
  Exposed-Modules:     Bio.RNAlienData
                       Bio.RNAlienLibrary
                       Bio.RNAcentralHTTP
                       Bio.InfernalParser