RNAlien/RNAlien.cabal at main · eggzilla/RNAlien · GitHub

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name:                RNAlien
version:             1.8.5
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@informatik.uni-freiburg.de
copyright:           Florian Eggenhofer
category:            Bioinformatics
build-type:          Simple
cabal-version:       >= 1.10.0
tested-with:         GHC == 8.8, GHC == 8.10, GHC == 9.0
Extra-Source-Files:
        README.md ChangeLog.md

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

source-repository this
  type:     git
  location: https://github.com/eggzilla/RNAlien/tree/1.8.5
  tag:      1.8.5

executable RNAlien
  Hs-Source-Dirs:      ./Biobase/
  main-is:	       RNAlien.hs
  ghc-options:         -Wall
  default-language:    Haskell2010
  other-modules:       Paths_RNAlien
  build-depends:       base >=4.5 && <5, cmdargs, directory,
                       random, containers, RNAlien, time, either-unwrap, filepath,
                       BiobaseFasta == 0.4.0.*, StockholmAlignment

executable RNAlienScan
  Hs-Source-Dirs:      ./Biobase/
  main-is:	       RNAlienScan.hs
  ghc-options:         -Wall
  default-language:    Haskell2010
  other-modules:       Paths_RNAlien
  build-depends:       base >=4.5 && <5, cmdargs, directory,
                       random, containers, RNAlien, time, either-unwrap, filepath,
                       BiobaseFasta == 0.4.0.*, StockholmAlignment

executable RNAlienStatistics
  Hs-Source-Dirs:      ./Biobase/
  main-is:             RNAlienStatistics.hs
  ghc-options:         -Wall
  default-language:    Haskell2010
  other-modules:       Paths_RNAlien
  build-depends:       base >=4.5 && <5, cmdargs, cassava, vector, process, bytestring,
                       either-unwrap, RNAlien, directory, split, filepath, ViennaRNAParser>=1.3.2,
                       BiobaseFasta == 0.4.0.*, BiobaseTypes == 0.2.1.*

executable cmsearchToBed
  Hs-Source-Dirs:      ./Biobase/
  main-is:             cmsearchToBED.hs
  ghc-options:         -Wall
  default-language:    Haskell2010
  other-modules:       Paths_RNAlien
  build-depends:       base >=4.5 && <5, cmdargs, either-unwrap, RNAlien, bytestring, text

executable RNAcentralHTTPRequest
  Hs-Source-Dirs:      ./Biobase/
  main-is:             RNAcentralHTTPRequest.hs
  ghc-options:         -Wall
  default-language:    Haskell2010
  other-modules:       Paths_RNAlien
  build-depends:       base >=4.5 && <5, cmdargs, either-unwrap, RNAlien

Library
  Hs-Source-Dirs:      .
  ghc-options:         -Wall -fno-warn-unused-do-bind -fsimpl-tick-factor=500
  default-language:    Haskell2010
  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory,
                       parsec, random, bytestring, Taxonomy >= 2.1.0, either-unwrap, containers,
                       ClustalParser>=1.3.0, vector, edit-distance, cassava, matrix, hierarchical-clustering,
                       filepath, HTTP, http-conduit, hxt, network<=2.8.0.0, aeson<=1.6.0.0, text, transformers,
                       pureMD5, http-types, text-metrics, BiobaseTypes == 0.2.1.*, BiobaseFasta == 0.4.0.*,
                       BiobaseBlast == 0.3.3.*, BlastHTTP >= 1.4.2, BiobaseHTTP == 1.2.0, silently, StockholmAlignment>=1.3.0, BiobaseEnsembl>=0.2.0.0, parallel, attoparsec
  Exposed-Modules:     Biobase.RNAlien.Types
                       Biobase.RNAlien.Library
                       Biobase.RNAlien.RNAcentralHTTP
                       Biobase.RNAlien.InfernalParser
                       Biobase.RNAlien.CMstatParser