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-rw-r--r--gnu/packages/bioinformatics.scm87
1 files changed, 87 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 43220d22fe..ab9dc185a3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -38,6 +38,7 @@
#:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system haskell)
#:use-module (guix build-system ocaml)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
@@ -72,6 +73,8 @@
#:use-module (gnu packages groff)
#:use-module (gnu packages guile)
#:use-module (gnu packages haskell)
+ #:use-module (gnu packages haskell-check)
+ #:use-module (gnu packages haskell-web)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
@@ -13970,3 +13973,87 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
Without filtering, users can perform (original) two-tailed or one-tailed
absolute GSEA.")
(license license:gpl2)))
+
+(define-public ngless
+ (package
+ (name "ngless")
+ (version "0.9.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/ngless/ngless.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117"))))
+ (build-system haskell-build-system)
+ (arguments
+ `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
+ ; error: parse error on input import
+ ; import Options.Applicative
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'create-cabal-file
+ (lambda _ (invoke "hpack") #t)))))
+ (inputs
+ `(("ghc-aeson" ,ghc-aeson)
+ ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+ ("ghc-async" ,ghc-async)
+ ("ghc-atomic-write" ,ghc-atomic-write)
+ ("ghc-bytestring-lexing" ,ghc-bytestring-lexing)
+ ("ghc-chart" ,ghc-chart)
+ ("ghc-chart-cairo" ,ghc-chart-cairo)
+ ("ghc-conduit" ,ghc-conduit)
+ ("ghc-conduit-algorithms" ,ghc-conduit-algorithms)
+ ("ghc-conduit-combinators" ,ghc-conduit-combinators)
+ ("ghc-conduit-extra" ,ghc-conduit-extra)
+ ("ghc-configurator" ,ghc-configurator)
+ ("ghc-convertible" ,ghc-convertible)
+ ("ghc-data-default" ,ghc-data-default)
+ ("ghc-double-conversion" ,ghc-double-conversion)
+ ("ghc-edit-distance" ,ghc-edit-distance)
+ ("ghc-either" ,ghc-either)
+ ("ghc-errors" ,ghc-errors)
+ ("ghc-extra" ,ghc-extra)
+ ("ghc-filemanip" ,ghc-filemanip)
+ ("ghc-file-embed" ,ghc-file-embed)
+ ("ghc-gitrev" ,ghc-gitrev)
+ ("ghc-hashtables" ,ghc-hashtables)
+ ("ghc-http-conduit" ,ghc-http-conduit)
+ ("ghc-inline-c" ,ghc-inline-c)
+ ("ghc-inline-c-cpp" ,ghc-inline-c-cpp)
+ ("ghc-intervalmap" ,ghc-intervalmap)
+ ("ghc-missingh" ,ghc-missingh)
+ ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+ ("ghc-parsec" ,ghc-parsec)
+ ("ghc-regex" ,ghc-regex)
+ ("ghc-safe" ,ghc-safe)
+ ("ghc-safeio" ,ghc-safeio)
+ ("ghc-strict" ,ghc-strict)
+ ("ghc-tar" ,ghc-tar)
+ ("ghc-text" ,ghc-text)
+ ("ghc-unliftio" ,ghc-unliftio)
+ ("ghc-unliftio-core" ,ghc-unliftio-core)
+ ("ghc-vector" ,ghc-vector)
+ ("ghc-yaml" ,ghc-yaml)
+ ("ghc-zlib" ,ghc-zlib)))
+ (propagated-inputs
+ `(("r-r6" ,r-r6)
+ ("r-hdf5r" ,r-hdf5r)
+ ("r-iterators" ,r-iterators)
+ ("r-itertools" ,r-itertools)
+ ("r-matrix" ,r-matrix)))
+ (native-inputs
+ `(("ghc-hpack" ,ghc-hpack)
+ ("ghc-quickcheck" ,ghc-quickcheck)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit",ghc-test-framework-hunit)
+ ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+ ("ghc-test-framework-th" ,ghc-test-framework-th)))
+ (home-page "https://gitlab.com/ngless/ngless")
+ (synopsis "DSL for processing next-generation sequencing data")
+ (description "Ngless is a domain-specific language for
+@dfn{next-generation sequencing} (NGS) data processing.")
+ (license license:expat)))