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gnu: ngless: Update to 1.0.1.

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* gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1.
[arguments]: Add a 'create-Versions.hs' phase that patches the Makefile
and invokes 'make' to generate a required file.
[inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and
'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib',
'ghc-diagrams-svg', and 'ghc-tar-conduit'.
This commit is contained in:
Timothy Sample 2019-11-13 22:59:24 -05:00
parent 74be1cb7b4
commit c1637311b6
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1 changed files with 24 additions and 6 deletions
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gnu/packages/bioinformatics.scm
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@ -13890,7 +13890,7 @@ (define-public jamm
(define-public ngless
(package
(name "ngless")
(version "0.9.1")
(version "1.0.1")
(source
(origin
(method git-fetch)
@ -13900,7 +13900,7 @@ (define-public ngless
(file-name (git-file-name name version))
(sha256
(base32
"0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117"))))
"06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg"))))
(build-system haskell-build-system)
(arguments
`(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
@ -13908,7 +13908,24 @@ (define-public ngless
; import Options.Applicative
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'create-cabal-file
(add-after 'unpack 'create-Versions.hs
(lambda _
(substitute* "Makefile"
(("BWA_VERSION = .*")
(string-append "BWA_VERSION = "
,(package-version bwa) "\n"))
(("SAM_VERSION = .*")
(string-append "SAM_VERSION = "
,(package-version samtools) "\n"))
(("PRODIGAL_VERSION = .*")
(string-append "PRODIGAL_VERSION = "
,(package-version prodigal) "\n"))
(("MINIMAP2_VERSION = .*")
(string-append "MINIMAP2_VERSION = "
,(package-version minimap2) "\n")))
(invoke "make" "NGLess/Dependencies/Versions.hs")
#t))
(add-after 'create-Versions.hs 'create-cabal-file
(lambda _ (invoke "hpack") #t))
;; These tools are expected to be installed alongside ngless.
(add-after 'install 'link-tools
@ -13937,15 +13954,15 @@ (define-public ngless
("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-diagrams-core" ,ghc-diagrams-core)
("ghc-diagrams-lib" ,ghc-diagrams-lib)
("ghc-diagrams-svg" ,ghc-diagrams-svg)
("ghc-double-conversion" ,ghc-double-conversion)
("ghc-edit-distance" ,ghc-edit-distance)
("ghc-either" ,ghc-either)
@ -13966,6 +13983,7 @@ (define-public ngless
("ghc-safeio" ,ghc-safeio)
("ghc-strict" ,ghc-strict)
("ghc-tar" ,ghc-tar)
("ghc-tar-conduit" ,ghc-tar-conduit)
("ghc-unliftio" ,ghc-unliftio)
("ghc-unliftio-core" ,ghc-unliftio-core)
("ghc-vector" ,ghc-vector)