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OrthoLang.cabal
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OrthoLang.cabal
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cabal-version: 2.2
name: OrthoLang
synopsis: Short, reproducible phylogenomic cuts
author: Jeffrey David Johnson
maintainer: [email protected]
version: 0.9.4
-- license: AGPL-3
license-file: LICENSE
build-type: Simple
data-files: examples/scripts/*.ol,
examples/gene-lists/*.txt,
examples/genome-lists/*.txt,
examples/sequences/*.fa,
examples/sequences/*.faa,
examples/sequences/*.fna,
examples/sequences/*.gbff,
examples/sequences/*.gbk,
docs/*.txt,
docs/modules/*.txt,
docs/types/*.txt,
docs/functions/*.txt,
tests/check/*.sh,
tests/versions/*.txt,
tests/repl/*.txt,
tests/scripts/*.ol,
tests/stdout/*.txt,
tests/tmpfiles/*.txt,
wrapper-scripts/*.sh
source-repository head
type: git
location: https://github.com/jefdaj/ortholang.git
common shared-properties
hs-source-dirs: .
default-language: Haskell2010
ghc-options:
-threaded
-rtsopts
-- TODO why does -N slow it down so much sometimes? remove?
-- TODO is there an optimal number/fraction of cores?
-- TODO does playing with flags for shake + other packages help?
-- TODO does -O2 help?
"-with-rtsopts=-N -IO"
-Wno-orphans
-- -pedantic
-- -O0
-- -O2
-- TODO what about the old shake -qg?
pkgconfig-depends: zlib
build-depends: Glob,
-- TODO is this ok to bring back? MissingH,
MissingH,
QuickCheck,
base,
bytestring,
configurator,
containers,
cryptohash,
directory,
data-default-class,
docopt,
-- exceptions,
-- enclosed-exceptions,
safe-exceptions,
-- TODO remove in favor of path
filelock,
filepath,
haskeline,
mtl,
parsec,
path,
path-io,
pretty,
process,
-- regex,
regex-compat,
regex-posix,
-- regex-pcre,
silently,
scientific,
shake >= 0.17.5,
split,
strict,
-- tagged-exception-core,
hspec,
tasty,
tasty-hunit,
tasty-hspec,
tasty-golden,
tasty-quickcheck,
temporary,
text,
transformers,
unbounded-delays,
unix,
utility-ht,
time,
concurrent-extra,
retry,
terminal-size,
posix-escape,
random,
random-shuffle,
dlist,
ansi-terminal,
setlocale,
raw-strings-qq,
logging,
progress-meter,
download
library
import: shared-properties
exposed-modules: Paths_OrthoLang,
OrthoLang.Core,
OrthoLang.Core.Actions,
OrthoLang.Core.Compile,
OrthoLang.Core.Compile.Basic,
OrthoLang.Core.Compile.Compose,
OrthoLang.Core.Compile.Map,
OrthoLang.Core.Compile.Map2,
OrthoLang.Core.Compile.Repeat,
OrthoLang.Core.Compile.Replace,
OrthoLang.Core.Config,
OrthoLang.Core.Eval,
OrthoLang.Core.Locks,
OrthoLang.Core.Parse,
OrthoLang.Core.Parse.Util,
OrthoLang.Core.Parse.Basic,
OrthoLang.Core.Parse.Expr,
OrthoLang.Core.Parse.Script,
OrthoLang.Core.Paths,
OrthoLang.Core.Pretty,
OrthoLang.Core.Repl,
OrthoLang.Core.Sanitize,
OrthoLang.Core.Types,
OrthoLang.Core.Util,
OrthoLang.Modules,
OrthoLang.Modules.BioMartR,
OrthoLang.Modules.Blast,
OrthoLang.Modules.BlastDB,
OrthoLang.Modules.BlastHits,
OrthoLang.Modules.BlastRBH,
OrthoLang.Modules.CRBBlast,
OrthoLang.Modules.Cheat,
OrthoLang.Modules.Diamond,
OrthoLang.Modules.Hmmer,
OrthoLang.Modules.ListLike,
OrthoLang.Modules.Load,
OrthoLang.Modules.MMSeqs,
OrthoLang.Modules.Math,
OrthoLang.Modules.Muscle,
OrthoLang.Modules.OrthoFinder,
OrthoLang.Modules.OrthoGroups,
OrthoLang.Modules.Busco,
OrthoLang.Modules.Permute,
OrthoLang.Modules.Plots,
OrthoLang.Modules.PsiBlast,
OrthoLang.Modules.Sample,
OrthoLang.Modules.Scores,
OrthoLang.Modules.SeqIO,
OrthoLang.Modules.Sets,
OrthoLang.Modules.SonicParanoid,
OrthoLang.Modules.Summarize,
OrthoLang.Modules.Range,
OrthoLang.Modules.SetsTable,
OrthoLang.Modules.AllVsAll,
OrthoLang.Modules.GreenCut,
OrthoLang.Test,
OrthoLang.Test.Versions
OrthoLang.Test.Parse,
OrthoLang.Test.Parse.Arbitrary,
OrthoLang.Test.Parse.Examples,
OrthoLang.Test.Repl,
OrthoLang.Test.Scripts
-- everything is built into one binary:
-- run tests with ortholang --test
-- write website reference docs with ortholang --reference
-- TODO is -IO -qg needed for ortholang, or just shake?
executable ortholang
import: shared-properties
main-is: OrthoLang.hs