diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,10 +1,13 @@ -# Table of Contents - -1. [Changelog for ELynx](#orgbba4466) +# Changelog for ELynx - +## Version 0.2.2 -# Changelog for ELynx +- Validation and repetition of previous analyses is finally possible with the + new `elynx` binary. +- A library `elynx-markov` for running Markov processes along phylogenetic trees + has been split off `elynx-seq`. This library performs the computations when + executing `slynx simulate ...`. +- Many other small improvements. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,18 +2,17 @@ # The ELynx Suite -Version: 0.1.0. +Version: 0.2.2. 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. +A Haskell library and tool set for computational biology. The goal of ELynx is +reproducible research. Evolutionary sequences and phylogenetic trees can be +read, viewed, modified and simulated. The command line with all arguments is +logged consistently, and automatically. Data integrity is verified using SHA256 +sums so that validation of past analyses is possible without the need to +recompute the result. -The Elynx Suite consists of four library packages and two executables providing +The Elynx Suite consists of four library packages and three executables providing a range of sub commands. The library packages are: @@ -25,8 +24,9 @@ The executables are: -- **slynx:** Analyze, modify, and simulate evolutionary sequences (FASTA format). -- **tlynx:** Analyze, modify, and simulate phylogenetic trees (Newick format). +- **slynx:** Analyze, modify, and simulate evolutionary sequences. +- **tlynx:** Analyze, modify, and simulate phylogenetic trees. +- **elynx:** Validate and redo past analyses. **ELynx is actively developed. We happily receive comments, ideas, feature requests, and pull requests!** @@ -68,10 +68,11 @@ slynx --help - ELynx Suite version 0.1.0. Developed by Dominik Schrempf. Compiled on March 21, - 2020, at 16:37 pm, UTC. + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. - Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] + Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND Analyze, and simulate multi sequence alignments. @@ -87,18 +88,17 @@ Available commands: concatenate Concatenate sequences found in input files. - examine Examine sequences. If data is a multi sequence - alignment, additionally analyze columns. + 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: + Available sequence file formats: - FASTA - Alphabet types: + Available alphabets: - DNA (nucleotides) - DNAX (nucleotides; including gaps) - DNAI (nucleotides; including gaps, and IUPAC codes) @@ -107,19 +107,20 @@ - 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. + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. slynx Analyze, modify, and simulate evolutionary sequences. tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. - Get help for specific commands: + Get help for sub commands: slynx examine --help @@ -129,13 +130,36 @@ slynx concatenate --help + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. Available options: + -h,--help Show this help text + -V,--version Show version -a,--alphabet NAME Specify alphabet type NAME INPUT-FILE Read sequences from INPUT-FILE -h,--help Show this help text + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Examine @@ -144,15 +168,37 @@ 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. + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] + Examine sequences. If data is a multi sequence alignment, additionally analyze columns. + Available options: + -h,--help Show this help text + -V,--version Show version -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 + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Filter @@ -161,12 +207,17 @@ slynx filter-rows --help - Usage: slynx filter-rows (-a|--alphabet NAME) [INPUT-FILE] - [--longer-than LENGTH] [--shorter-than LENGTH] - [--standard-characters] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + 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: + -h,--help Show this help text + -V,--version Show version -a,--alphabet NAME Specify alphabet type NAME INPUT-FILE Read sequences from INPUT-FILE --longer-than LENGTH Only keep sequences longer than LENGTH @@ -174,21 +225,61 @@ --standard-characters Only keep sequences containing at least one standard (i.e., non-IUPAC) character -h,--help Show this help text + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help Filter columns of multi sequence alignments with `filter-columns`. slynx filter-columns --help - Usage: slynx filter-columns (-a|--alphabet NAME) [INPUT-FILE] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] - Filter columns of multi-sequence alignments. + Filter columns of multi sequence alignments. Available options: + -h,--help Show this help text + -V,--version Show version -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 + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Simulate @@ -197,16 +288,22 @@ 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,...]"] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + 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 + -h,--help Show this help text + -V,--version Show version + -t,--tree-file Name Read tree from Newick file NAME -s,--substitution-model MODEL Set the phylogenetic substitution model; available models are shown below (mutually exclusive with -m @@ -228,17 +325,24 @@ Substitution models: -s "MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}" - Supported DNA models: JC, HKY. + Supported DNA models: JC, F81, HKY, GTR4. For example, -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE} - Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom. + -s GTR4[e_AC,e_AG,e_AT,e_CG,e_CT,e_GT]{DOUBLE,DOUBLE,DOUBLE,DOUBLE} + where the 'e_XY' are the exchangeabilities from nucleotide X to Y. + Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom, GTR20. MODEL-Custom means that only the exchangeabilities of MODEL are used, and a custom stationary distribution is provided. For example, + -s LG -s LG-Custom{...} + -s GTR20[e_AR,e_AN,...]{...} + the 'e_XY' are the exchangeabilities from amino acid X to Y (alphabetical order). + Notes: The F81 model for DNA is equivalent to the Poisson-Custom for proteins. + The GTR4 model for DNA is equivalent to the GTR20 for proteins. Mixture models: - -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2)" + -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2[PARAMETERS]{STATIONARY_DISTRIBUTION},...)" 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. @@ -253,6 +357,22 @@ LG exchangeabilities with stationary distributions given in FILE. -m "EDM(LG-Custom)" -e FILE For special mixture models, mixture weights are optional. + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Sub-sample @@ -261,12 +381,18 @@ slynx sub-sample --help - Usage: slynx sub-sample (-a|--alphabet NAME) [INPUT-FILE] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + 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: + -h,--help Show this help text + -V,--version Show version -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 @@ -276,8 +402,23 @@ 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. + 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. + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Translate @@ -286,17 +427,40 @@ slynx translate --help - Usage: slynx translate (-a|--alphabet NAME) [INPUT-FILE] - (-r|--reading-frame INT) (-u|--universal-code CODE) + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + 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: + -h,--help Show this help text + -V,--version Show version -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 + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help # TLynx @@ -305,10 +469,11 @@ tlynx --help - ELynx Suite version 0.1.0. Developed by Dominik Schrempf. Compiled on March 21, - 2020, at 16:37 pm, UTC. + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. - Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] + Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND Compare, examine, and simulate phylogenetic trees. @@ -323,37 +488,33 @@ 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). + 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). + 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 + Available tree file formats: + - Newick Standard: Branch support values are stored in square brackets after branch lengths. + - Newick IqTree: Branch support values are stored as node names after the closing bracket of forests. + - Newick RevBayes Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are IGNORED at the moment. - 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. + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. slynx Analyze, modify, and simulate evolutionary sequences. tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. - Get help for specific commands: + Get help for sub commands: slynx examine --help @@ -363,18 +524,43 @@ tlynx compare --help - Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-i|--newick-iqtree] - NAME - Compare two phylogenetic trees (compute distances and branch-wise - differences). + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] + [-f|--newick-format FORMAT] NAME + Compare two phylogenetic trees (compute distances and branch-wise differences). + Available options: + -h,--help Show this help text + -V,--version Show version -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) + -b,--bipartitions Print and plot common and missing bipartitions + -t,--intersect Compare intersections; i.e., before comparison, drop + leaves that are not present in the other tree + -f,--newick-format FORMAT + Newick tree format; see 'tlynx + --help' (default: Standard) NAME Tree file -h,--help Show this help text + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Examine @@ -383,14 +569,38 @@ tlynx examine --help - Usage: tlynx examine [INPUT-FILE] [-i|--newick-iqtree] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. Available options: + -h,--help Show this help text + -V,--version Show version INPUT-FILE Read trees from INPUT-FILE - -i,--newick-iqtree Use IQ-TREE Newick format (internal node labels are - branch support values) + -f,--newick-format FORMAT + Newick tree format; see 'tlynx + --help' (default: Standard) -h,--help Show this help text + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help ## Simulate @@ -399,13 +609,19 @@ 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] + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + 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. + Simulate phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process). Available options: + -h,--help Show this help text + -V,--version Show version -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) @@ -424,8 +640,63 @@ 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 + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help +# ELynx + +Validate and (optionally) redo past ELynx analyses. + + elynx --help + + ELynx Suite version 0.2.1. + Developed by Dominik Schrempf. + Compiled on April 27, 2020, at 12:08 pm, UTC. + + Usage: elynx COMMAND + Validate and redo past ELynx analyses + + Available options: + -h,--help Show this help text + -V,--version Show version + + Available commands: + validate Validate an ELynx analysis + redo Redo an ELynx analysis + + + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. + + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. + + Get help for sub commands: + slynx examine --help + + # Library documentation Documentation of the libraries can be found on [Hackage](https://hackage.haskell.org/): @@ -435,8 +706,9 @@ - [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: +Documentation of the executables is also available: +- [elynx](https://hackage.haskell.org/package/elynx) - [slynx](https://hackage.haskell.org/package/slynx) - [tlynx](https://hackage.haskell.org/package/tlynx) diff --git a/app/Main.hs b/app/Main.hs --- a/app/Main.hs +++ b/app/Main.hs @@ -166,7 +166,7 @@ runRedo :: RedoArguments -> IO () runRedo a = do let fp = rElynxFile a - let f = rForce 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." diff --git a/elynx.cabal b/elynx.cabal --- a/elynx.cabal +++ b/elynx.cabal @@ -1,6 +1,6 @@ cabal-version: 1.12 name: elynx -version: 0.2.1 +version: 0.2.2 license: GPL-3 license-file: LICENSE copyright: Dominik Schrempf (2020) @@ -34,7 +34,7 @@ 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, + elynx-tools >=0.2.2 && <0.3, optparse-applicative >=0.15.1.0 && <0.16, - slynx >=0.2.1 && <0.3, - tlynx >=0.2.1 && <0.3 + slynx >=0.2.2 && <0.3, + tlynx >=0.2.2 && <0.3