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gnu: ngless: Use gexp.

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* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
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Ricardo Wurmus 2023-01-06 13:56:34 +01:00
parent 648c370f33
commit e20ca244db
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1 changed files with 36 additions and 35 deletions
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gnu/packages/bioinformatics.scm
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@ -14171,41 +14171,42 @@ datasets.")
(patches (search-patches "ngless-unliftio.patch")))) (patches (search-patches "ngless-unliftio.patch"))))
(build-system haskell-build-system) (build-system haskell-build-system)
(arguments (arguments
`(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: (list
; error: parse error on input import #:haddock? #f ;The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
; import Options.Applicative ;error: parse error on input import
#:phases ;import Options.Applicative
(modify-phases %standard-phases #:phases
(add-after 'unpack 'create-Versions.hs #~(modify-phases %standard-phases
(lambda _ (add-after 'unpack 'create-Versions.hs
(substitute* "Makefile" (lambda _
(("BWA_VERSION = .*") (substitute* "Makefile"
(string-append "BWA_VERSION = " (("BWA_VERSION = .*")
,(package-version bwa) "\n")) (string-append "BWA_VERSION = "
(("SAM_VERSION = .*") #$(package-version bwa) "\n"))
(string-append "SAM_VERSION = " (("SAM_VERSION = .*")
,(package-version samtools) "\n")) (string-append "SAM_VERSION = "
(("PRODIGAL_VERSION = .*") #$(package-version samtools) "\n"))
(string-append "PRODIGAL_VERSION = " (("PRODIGAL_VERSION = .*")
,(package-version prodigal) "\n")) (string-append "PRODIGAL_VERSION = "
(("MINIMAP2_VERSION = .*") #$(package-version prodigal) "\n"))
(string-append "MINIMAP2_VERSION = " (("MINIMAP2_VERSION = .*")
,(package-version minimap2) "\n"))) (string-append "MINIMAP2_VERSION = "
(invoke "make" "NGLess/Dependencies/Versions.hs"))) #$(package-version minimap2) "\n")))
(add-after 'create-Versions.hs 'create-cabal-file (invoke "make" "NGLess/Dependencies/Versions.hs")))
(lambda _ (invoke "hpack"))) (add-after 'create-Versions.hs 'create-cabal-file
;; These tools are expected to be installed alongside ngless. (lambda _ (invoke "hpack")))
(add-after 'install 'link-tools ;; These tools are expected to be installed alongside ngless.
(lambda* (#:key inputs outputs #:allow-other-keys) (add-after 'install 'link-tools
(let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (lambda* (#:key inputs #:allow-other-keys)
(symlink (search-input-file inputs "/bin/prodigal") (let ((bin (string-append #$output "/bin/")))
(string-append bin "ngless-" ,version "-prodigal")) (symlink (search-input-file inputs "/bin/prodigal")
(symlink (search-input-file inputs "/bin/minimap2") (string-append bin "ngless-" #$version "-prodigal"))
(string-append bin "ngless-" ,version "-minimap2")) (symlink (search-input-file inputs "/bin/minimap2")
(symlink (search-input-file inputs "/bin/samtools") (string-append bin "ngless-" #$version "-minimap2"))
(string-append bin "ngless-" ,version "-samtools")) (symlink (search-input-file inputs "/bin/samtools")
(symlink (search-input-file inputs "/bin/bwa") (string-append bin "ngless-" #$version "-samtools"))
(string-append bin "ngless-" ,version "-bwa")))))))) (symlink (search-input-file inputs "/bin/bwa")
(string-append bin "ngless-" #$version "-bwa"))))))))
(inputs (inputs
(list prodigal (list prodigal
bwa bwa