elynx (empty) → 0.2.1
raw patch · 6 files changed
+1450/−0 lines, 6 filesdep +aesondep +basedep +bytestring
Dependencies added: aeson, base, bytestring, elynx-tools, optparse-applicative, slynx, tlynx
Files
- ChangeLog.md +10/−0
- LICENSE +674/−0
- README.md +442/−0
- app/Main.hs +196/−0
- app/Options.hs +88/−0
- elynx.cabal +40/−0
+ ChangeLog.md view
@@ -0,0 +1,10 @@++# Table of Contents++1. [Changelog for ELynx](#orgbba4466)+++<a id="orgbba4466"></a>++# Changelog for ELynx+
+ LICENSE view
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+ README.md view
@@ -0,0 +1,442 @@+++# The ELynx Suite++Version: 0.1.0.+Reproducible evolution made easy.++The ELynx Suite is a Haskell library and a tool set for computational biology.+The goal of the ELynx Suite is reproducible research. Evolutionary sequences and+phylogenetic trees can be read, viewed, modified and simulated. Exact+specification of all options is necessary, and nothing is assumed about the data+(e.g., the type of the genetic code). The command line with all arguments is+consistently, and automatically logged. The work overhead in the beginning+usually pays off in the end.++The Elynx Suite consists of four library packages and two executables providing+a range of sub commands.++The library packages are:++- **elynx-markov:** Simulate multi sequence alignments along phylogenetic trees.+- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments.+- **elynx-tools:** Tools for the provided executables.+- **elynx-tree:** Handle phylogenetic trees.++The executables are:++- **slynx:** Analyze, modify, and simulate evolutionary sequences (FASTA format).+- **tlynx:** Analyze, modify, and simulate phylogenetic trees (Newick format).++**ELynx is actively developed. We happily receive comments, ideas, feature+requests, and pull requests!**+++# Installation++ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/).++1. Install Stack with your package manager, or directly from the web+ page.+ + curl -sSL https://get.haskellstack.org/ | sh++2. Clone the ELynx repository.+ + git clone clone https://github.com/dschrempf/elynx++3. Navigate to the newly created `elynx` folder and build the binaries.+ This will take a while.+ + stack build++4. Run a binary from within the project directory. For example,+ + stack exec tlynx -- --help++5. If needed, install the binaries.+ + stack install+ + The binaries are installed into `~/.local/bin/` which has to be added to the+ [PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.+++# SLynx++Handle evolutionary sequences.++ slynx --help++ ELynx Suite version 0.1.0. Developed by Dominik Schrempf. Compiled on March 21,+ 2020, at 16:37 pm, UTC.+ + Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]+ [-f|--force] COMMAND+ Analyze, and simulate multi sequence alignments.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info+ Debug (default: Info)+ -o,--output-file-basename NAME+ Specify base name of output file+ -f,--force Ignore previous analysis and overwrite existing+ output files.+ + Available commands:+ concatenate Concatenate sequences found in input files.+ examine Examine sequences. If data is a multi sequence+ alignment, additionally analyze columns.+ filter-columns Filter columns of multi sequence alignments.+ filter-rows Filter rows (or sequences) found in input files.+ simulate Simulate multi sequence alignments.+ sub-sample Sub-sample columns from multi sequence alignments.+ translate Translate from DNA to Protein or DNAX to ProteinX.+ + File formats:+ - FASTA+ + Alphabet types:+ - DNA (nucleotides)+ - DNAX (nucleotides; including gaps)+ - DNAI (nucleotides; including gaps, and IUPAC codes)+ - Protein (amino acids)+ - ProteinX (amino acids; including gaps)+ - ProteinS (amino acids; including gaps, and translation stops)+ - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)+ + The ELynx Suite+ ---------------+ A Haskell library and a tool set for computational biology. The goal of the+ ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic+ trees can be read, viewed, modified and simulated. Exact specification of all+ options is necessary, and nothing is assumed about the data (e.g., the type of+ code). The command line with all arguments is consistently, and automatically+ logged.+ + slynx Analyze, modify, and simulate evolutionary sequences.+ tlynx Analyze, modify, and simulate phylogenetic trees.+ + Get help for specific commands:+ slynx examine --help+++## Concatenate++Concatenate multi sequence alignments.++ slynx concatenate --help++ Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE+ Concatenate sequences found in input files.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -h,--help Show this help text+++## Examine++Examine sequence with `slynx examine`.++ slynx examine --help++ Usage: slynx examine (-a|--alphabet NAME) [INPUT-FILE] [--per-site]+ Examine sequences. If data is a multi sequence alignment, additionally analyze+ columns.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --per-site Report per site summary statistics+ -h,--help Show this help text+++## Filter++Filter sequences with `filer-rows`.++ slynx filter-rows --help++ Usage: slynx filter-rows (-a|--alphabet NAME) [INPUT-FILE]+ [--longer-than LENGTH] [--shorter-than LENGTH]+ [--standard-characters]+ Filter rows (or sequences) found in input files.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --longer-than LENGTH Only keep sequences longer than LENGTH+ --shorter-than LENGTH Only keep sequences shorter than LENGTH+ --standard-characters Only keep sequences containing at least one standard+ (i.e., non-IUPAC) character+ -h,--help Show this help text++Filter columns of multi sequence alignments with `filter-columns`.++ slynx filter-columns --help++ Usage: slynx filter-columns (-a|--alphabet NAME) [INPUT-FILE]+ [--standard-chars DOUBLE]+ Filter columns of multi-sequence alignments.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --standard-chars DOUBLE Keep columns with a proportion standard (non-IUPAC)+ characters larger than DOUBLE in [0,1]+ -h,--help Show this help text+++## Simulate++Simulate sequences with `slynx simulate`.++ slynx simulate --help++ Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]+ [-m|--mixture-model MODEL] [-e|--edm-file NAME]+ [-p|--siteprofile-files NAMES]+ [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]+ [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]+ (-l|--length NUMBER) [-S|--seed [INT]]+ Simulate multi sequence alignments.+ + Available options:+ -t,--tree-file Name Read trees from file NAME+ -s,--substitution-model MODEL+ Set the phylogenetic substitution model; available+ models are shown below (mutually exclusive with -m+ option)+ -m,--mixture-model MODEL Set the phylogenetic mixture model; available models+ are shown below (mutually exclusive with -s option)+ -e,--edm-file NAME Empirical distribution model file NAME in Phylobayes+ format+ -p,--siteprofile-files NAMES+ File names of site profiles in Phylobayes format+ -w,--mixture-model-weights "[DOUBLE,DOUBLE,...]"+ Weights of mixture model components+ -g,--gamma-rate-heterogeneity "(NCAT,SHAPE)"+ Number of gamma rate categories and shape parameter+ -l,--length NUMBER Set alignment length to NUMBER+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text+ + Substitution models:+ -s "MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}"+ Supported DNA models: JC, HKY.+ For example,+ -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}+ Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom.+ MODEL-Custom means that only the exchangeabilities of MODEL are used,+ and a custom stationary distribution is provided.+ For example,+ -s LG-Custom{...}+ + Mixture models:+ -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2)"+ For example,+ -m "MIXTURE(JC,HKY[6.0]{0.3,0.2,0.2,0.3})"+ Mixture weights have to be provided with the -w option.+ + Special mixture models:+ -m CXX+ where XX is 10, 20, 30, 40, 50, or 60; CXX models, Quang et al., 2008.+ -m "EDM(EXCHANGEABILITIES)"+ Arbitrary empirical distribution mixture (EDM) models.+ Stationary distributions have to be provided with the -e option.+ For example,+ LG exchangeabilities with stationary distributions given in FILE.+ -m "EDM(LG-Custom)" -e FILE+ For special mixture models, mixture weights are optional.+++## Sub-sample++Sub-sample columns from multi sequence alignments.++ slynx sub-sample --help++ Usage: slynx sub-sample (-a|--alphabet NAME) [INPUT-FILE]+ (-n|--number-of-sites INT)+ (-m|--number-of-alignments INT) [-S|--seed [INT]]+ Sub-sample columns from multi sequence alignments.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -n,--number-of-sites INT Number of sites randomly drawn with replacement+ -m,--number-of-alignments INT+ Number of multi sequence alignments to be created+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text+ + Create a given number of multi sequence alignments, each of which contains a+ given number of random sites drawn from the original multi sequence alignment.+++## Translate++Translate sequences.++ slynx translate --help++ Usage: slynx translate (-a|--alphabet NAME) [INPUT-FILE]+ (-r|--reading-frame INT) (-u|--universal-code CODE)+ Translate from DNA to Protein or DNAX to ProteinX.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -r,--reading-frame INT Reading frame [0|1|2].+ -u,--universal-code CODE universal code; one of: Standard,+ VertebrateMitochondrial.+ -h,--help Show this help text+++# TLynx++Handle phylogenetic trees in Newick format.++ tlynx --help++ ELynx Suite version 0.1.0. Developed by Dominik Schrempf. Compiled on March 21,+ 2020, at 16:37 pm, UTC.+ + Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]+ [-f|--force] COMMAND+ Compare, examine, and simulate phylogenetic trees.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info+ Debug (default: Info)+ -o,--output-file-basename NAME+ Specify base name of output file+ -f,--force Ignore previous analysis and overwrite existing+ output files.+ + Available commands:+ coalesce Simulate phylogenetic trees using the coalescent+ processes (see also the 'simulate' command for+ simulations using the birth and death process).+ compare Compare two phylogenetic trees (compute distances and+ branch-wise differences).+ connect Connect two phylogenetic trees in all ways (possibly+ honoring constraints).+ distance Compute distances between many phylogenetic trees.+ examine Compute summary statistics of phylogenetic trees.+ shuffle Shuffle a phylogenetic tree (keep coalescent times,+ but shuffle topology and leaves).+ simulate Simulate phylogenetic trees using birth and death+ processes (see also the 'coalesce' command for+ simulations using the coalescent process).+ + File formats:+ - Newick+ + The ELynx Suite+ ---------------+ A Haskell library and a tool set for computational biology. The goal of the+ ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic+ trees can be read, viewed, modified and simulated. Exact specification of all+ options is necessary, and nothing is assumed about the data (e.g., the type of+ code). The command line with all arguments is consistently, and automatically+ logged.+ + slynx Analyze, modify, and simulate evolutionary sequences.+ tlynx Analyze, modify, and simulate phylogenetic trees.+ + Get help for specific commands:+ slynx examine --help+++## Compare++Compute distances between phylogenetic trees.++ tlynx compare --help++ Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-i|--newick-iqtree]+ NAME+ Compare two phylogenetic trees (compute distances and branch-wise+ differences).+ + Available options:+ -n,--normalize Normalize trees before comparison+ -b,--bipartitions Print common and missing bipartitions+ -i,--newick-iqtree Use IQ-TREE Newick format (internal node labels are+ branch support values)+ NAME Tree file+ -h,--help Show this help text+++## Examine++Compute summary statistics of phylogenetic trees.++ tlynx examine --help++ Usage: tlynx examine [INPUT-FILE] [-i|--newick-iqtree]+ Compute summary statistics of phylogenetic trees.+ + Available options:+ INPUT-FILE Read trees from INPUT-FILE+ -i,--newick-iqtree Use IQ-TREE Newick format (internal node labels are+ branch support values)+ -h,--help Show this help text+++## Simulate++Simulate phylogenetic trees using birth and death processes.++ tlynx simulate --help++ Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE]+ [-M|--condition-on-mrca] [-l|--lambda DOUBLE]+ [-m|--mu DOUBLE] [-r|--rho DOUBLE] [-u|--sub-sample]+ [-s|--summary-statistics] [-S|--seed [INT]]+ Simulate phylogenetic trees using birth and death processes.+ + Available options:+ -t,--nTrees INT Number of trees (default: 10)+ -n,--nLeaves INT Number of leaves per tree (default: 5)+ -H,--height DOUBLE Fix tree height (no default)+ -M,--condition-on-mrca Do not condition on height of origin but on height of+ MRCA+ -l,--lambda DOUBLE Birth rate lambda (default: 1.0)+ -m,--mu DOUBLE Death rate mu (default: 0.9)+ -r,--rho DOUBLE Sampling probability rho (default: 1.0)+ -u,--sub-sample Perform sub-sampling; see below.+ -s,--summary-statistics Only output number of children for each branch+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text+ + Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate.+ Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character.+ Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again.+ Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005+++# Library documentation++Documentation of the libraries can be found on [Hackage](https://hackage.haskell.org/):++- [elynx-markov](https://hackage.haskell.org/package/elynx-markov)+- [elynx-seq](https://hackage.haskell.org/package/elynx-seq)+- [elynx-tools](https://hackage.haskell.org/package/elynx-tools)+- [elynx-tree](https://hackage.haskell.org/package/elynx-tree)++Documentation of the executables is, or course, also available:++- [slynx](https://hackage.haskell.org/package/slynx)+- [tlynx](https://hackage.haskell.org/package/tlynx)+
+ app/Main.hs view
@@ -0,0 +1,196 @@+{-# LANGUAGE ScopedTypeVariables #-}+{-# LANGUAGE TypeApplications #-}+{-# LANGUAGE OverloadedStrings #-}++{- |+Module : Main+Description : Validate elynx file+Copyright : (c) Dominik Schrempf 2020+License : GPL-3.0-or-later++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Wed Apr 22 21:08:25 2020.++-}++module Main+ ( main+ )+where++import Control.Monad+import Data.Aeson+import qualified Data.Aeson.Types as J+import qualified Data.ByteString.Char8 as B+import Data.Maybe+import Data.Version ( Version )+import Options.Applicative+import System.Environment ( withProgName+ , withArgs+ )++import ELynx.Tools++import SLynx.SLynx ( slynx )+import qualified SLynx.Options as S+import TLynx.TLynx ( tlynx )+import qualified TLynx.Options as T++import Options++parseProgName :: Value -> J.Parser String+parseProgName = withObject "progName" $ \o -> o .: "progName"++-- TODO: Declaring program names here should not be necessary.+parseAllR :: String -> Value -> J.Parser AllReproductions+parseAllR "slynx" v =+ S <$> (parseJSON v :: J.Parser (Reproduction (Arguments S.CommandArguments)))+parseAllR "tlynx" v =+ T <$> (parseJSON v :: J.Parser (Reproduction (Arguments T.CommandArguments)))+parseAllR p _ =+ let err = unlines+ [ "Could not parse program name:"+ , p+ , "Do you use the correct ELynx version?"+ ]+ in error err++parse :: Show a => [String] -> Parser a -> a+parse s p = fromMaybe+ (error $ "parse: could not parse command line arguments: " ++ show s)+ (getParseResult res)+ where res = execParserPure defaultPrefs (info p briefDesc) s++-- Does the command line fit the saved arguments?+checkArgs+ :: forall a+ . (Eq a, Show a, Reproducible a)+ => Reproduction a+ -> IO (Either String ())+checkArgs s = do+ let r = reproducible s+ p = parser @a+ as = argsStr s+ res = parse as p+ return $ if res /= reproducible s+ then Left $ unlines+ ["Command line string and command arguments do not fit:", show as, show r]+ else Right ()++-- Does the file match the base 16 checksum?+checkFile :: FilePath -> B.ByteString -> IO (Either String ())+checkFile fp h = do+ h' <- hashFile fp+ return $ if h' == h+ then Right ()+ else Left $ unlines+ [ "SHA256 sum does not match for a file:"+ , fp ++ " has check sum " ++ B.unpack h'+ , "Stored check sum is " ++ B.unpack h+ ]++checkVersion :: Version -> Either String ()+checkVersion v = if v == version+ then Right ()+ else Left $ unlines+ [ "Versions differ:"+ , "Version in ELynx reproduction file: " ++ show v+ , "Version of current executable: " ++ show version+ ]++checkHash :: Reproducible a => Reproduction a -> Either String ()+checkHash r = if h == h'+ then Right ()+ else Left $ unlines+ [ "ELynx reproduction file has been changed:"+ , "Hash saved in file: " ++ show h+ , "Hash calculated from file: " ++ show h'+ ]+ where+ h = rHash r+ h' = Just $ getReproductionHash r++-- Check if command line arguments and files check sums are matching.+validate+ :: (Eq a, Show a, Reproducible a) => Reproduction a -> IO (Either String ())+validate s = do+ chA <- checkArgs s+ let chV = checkVersion (rVersion s)+ chH = checkHash s+ chFs <- zipWithM checkFile (files s) (map B.pack $ checkSums s)+ return $ sequence_ (chA : chV : chH : chFs)++validateAllReproductions :: AllReproductions -> IO (Either String ())+validateAllReproductions (S x) = validate x+validateAllReproductions (T x) = validate x++getAllR :: FilePath -> IO AllReproductions+getAllR fp = do+ eELynx <- eitherDecodeFileStrict fp :: IO (Either String Value)+ elynx <- case eELynx of+ Left err -> do+ putStrLn "Failed decoding the ELynx reproduction file."+ putStrLn "The following error occurred:"+ error err+ Right val -> return val+ prog <- case J.parseEither parseProgName elynx of+ Left err -> do+ putStrLn "Failed getting command hash from ELynx reproduction file."+ putStrLn "The following error occurred:"+ error err+ Right prog -> return prog+ case J.parseEither (parseAllR prog) elynx of+ Left err -> do+ putStrLn "Failed parsing the ELynx reproduction file."+ putStrLn "The following error occurred:"+ error err+ Right repr -> return repr++-- Read and validate ELynx reproduction file. Check consistency of arguments and+-- input files.+runValidate :: ValidateArguments -> IO ()+runValidate a = do+ let fp = vElynxFile a+ repr <- getAllR fp+ val <- validateAllReproductions repr+ case val of+ Left err -> do+ putStrLn "Failed validating the ELynx reproduction file."+ putStrLn "The following error occurred:"+ error err+ Right () -> putStrLn "Validation successful!"++runRedo :: RedoArguments -> IO ()+runRedo a = do+ let fp = rElynxFile a+ let f = rForce a+ when (f == Force False) $ do+ putStrLn "Validate ELynx reproduction file before reanalysis."+ putStrLn "Use the --force (-f) option to skip this test."+ runValidate (ValidateArguments fp)+ repr <- getAllR fp+ let as = getArgs repr+ as' <- if "-f" `notElem` as && "--force" `notElem` as+ then do+ putStrLn+ "Force option required to redo analysis. Add -f (force) to arguments."+ return $ "-f" : as+ else return as+ withProgName (getProgName repr) $ withArgs as' $ redo repr++setForce :: Arguments a -> Arguments a+setForce (Arguments g l) = Arguments g { forceReanalysis = Force True } l++redo :: AllReproductions -> IO ()+redo (S x) = slynx $ setForce $ reproducible x+redo (T x) = tlynx $ setForce $ reproducible x++main :: IO ()+main = do+ g <- execParser commandArguments+ case g of+ Validate a -> runValidate a+ Redo a -> runRedo a
+ app/Options.hs view
@@ -0,0 +1,88 @@+{-# LANGUAGE DeriveGeneric #-}++{- |+Module : Options+Description : Options for elynx validation and redo sub commands+Copyright : (c) Dominik Schrempf 2020+License : GPL-3.0-or-later++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Apr 23 19:17:17 2020.++-}++module Options+ ( AllReproductions(..)+ , getProgName+ , getArgs+ , ValidateArguments(..)+ , RedoArguments(..)+ , CommandArguments(..)+ , commandArguments+ )+where++import Options.Applicative++import ELynx.Tools++import qualified SLynx.Options as S+import qualified TLynx.Options as T++-- | Collect all reproductions in one data type.+data AllReproductions = S (Reproduction (Arguments S.CommandArguments))+ | T (Reproduction (Arguments T.CommandArguments))++-- | Get program name irrespective of which program has been run.+getProgName :: AllReproductions -> String+getProgName (S x) = progName x+getProgName (T x) = progName x++-- | Get arguments irrespective of which program has been run.+getArgs :: AllReproductions -> [String]+getArgs (S x) = argsStr x+getArgs (T x) = argsStr x++newtype ValidateArguments = ValidateArguments+ { vElynxFile :: FilePath }+ deriving (Eq, Show, Generic)++validateArguments :: Parser ValidateArguments+validateArguments = ValidateArguments <$> inFileArg++validateDsc :: [String]+validateDsc = ["Validate an ELynx analysis"]++data RedoArguments = RedoArguments+ { rElynxFile :: FilePath+ , rForce :: Force }+ deriving (Eq, Show, Generic)++redoArguments :: Parser RedoArguments+redoArguments = RedoArguments <$> inFileArg <*> forceOpt++redoDsc :: [String]+redoDsc = ["Redo an ELynx analysis"]++inFileArg :: Parser FilePath+inFileArg = strArgument $ metavar "ELYNX-FILE"++data CommandArguments = Validate ValidateArguments+ | Redo RedoArguments++validateCommand :: Mod CommandFields CommandArguments+validateCommand =+ createCommand "validate" validateDsc [] validateArguments Validate++redoCommand :: Mod CommandFields CommandArguments+redoCommand = createCommand "redo" redoDsc [] redoArguments Redo++commandArguments :: ParserInfo CommandArguments+commandArguments =+ elynxParserInfo desc [] $ hsubparser $ validateCommand <> redoCommand++desc :: [String]+desc = ["Validate and redo past ELynx analyses"]
+ elynx.cabal view
@@ -0,0 +1,40 @@+cabal-version: 1.12+name: elynx+version: 0.2.1+license: GPL-3+license-file: LICENSE+copyright: Dominik Schrempf (2020)+maintainer: dominik.schrempf@gmail.com+author: Dominik Schrempf+homepage: https://github.com/dschrempf/elynx#readme+bug-reports: https://github.com/dschrempf/elynx/issues+synopsis: Validate and (optionally) redo ELynx analyses+description:+ Please see the README on GitHub at <https://github.com/dschrempf/elynx>.+category: Bioinformatics+build-type: Simple+extra-source-files:+ README.md+ ChangeLog.md++source-repository head+ type: git+ location: https://github.com/dschrempf/elynx++executable elynx+ main-is: Main.hs+ hs-source-dirs: app+ other-modules:+ Options+ Paths_elynx+ default-language: Haskell2010+ ghc-options: -Wall -fllvm -threaded -rtsopts -with-rtsopts=-N+ -fwrite-ide-info+ build-depends:+ aeson >=1.4.7.1 && <1.5,+ base >=4.13.0.0 && <4.14,+ bytestring >=0.10.10.0 && <0.11,+ elynx-tools >=0.2.1 && <0.3,+ optparse-applicative >=0.15.1.0 && <0.16,+ slynx >=0.2.1 && <0.3,+ tlynx >=0.2.1 && <0.3