slynx 0.3.1 → 0.3.2
raw patch · 4 files changed
+41/−39 lines, 4 filessetup-changed
Files
- ChangeLog.md +7/−1
- README.md +27/−27
- Setup.hs +2/−0
- slynx.cabal +5/−11
ChangeLog.md view
@@ -2,7 +2,13 @@ # Changelog for ELynx -## Version 0.3.2; in development+## Unreleased changes+++## Version 0.3.2++- Remove llvm dependency.+- Move away from hpack. ## Version 0.3.1
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.1.+Version: 0.3.2. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -90,9 +90,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND@@ -136,9 +136,9 @@ slynx concatenate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files.@@ -157,9 +157,9 @@ slynx examine --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns.@@ -179,9 +179,9 @@ slynx filter-rows --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters]@@ -202,9 +202,9 @@ slynx filter-columns --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE]@@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -305,9 +305,9 @@ slynx sub-sample --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT)@@ -335,9 +335,9 @@ slynx translate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE)@@ -360,9 +360,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND@@ -399,9 +399,9 @@ tlynx compare --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES@@ -428,9 +428,9 @@ tlynx examine --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees.@@ -452,9 +452,9 @@ tlynx simulate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] @@ -491,9 +491,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
slynx.cabal view
@@ -1,13 +1,6 @@-cabal-version: 2.2---- This file has been generated from package.yaml by hpack version 0.34.2.------ see: https://github.com/sol/hpack------ hash: 286f8b4edbcbe74a920bfa98bfeb769b685b7591ba79d26c1a024faa2889e888-+cabal-version: 2.2 name: slynx-version: 0.3.1+version: 0.3.2 synopsis: Handle molecular sequences description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category: Bioinformatics@@ -19,6 +12,7 @@ license: GPL-3.0-or-later license-file: LICENSE build-type: Simple+ extra-source-files: README.md ChangeLog.md@@ -51,7 +45,7 @@ Paths_slynx hs-source-dirs: src- ghc-options: -Wall -fllvm+ ghc-options: -Wall build-depends: async , attoparsec@@ -77,7 +71,7 @@ Paths_slynx hs-source-dirs: app- ghc-options: -Wall -fllvm -threaded -rtsopts -with-rtsopts=-N+ ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N build-depends: base >=4.7 && <5 , slynx