mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
Upgrade Haskell packages.
Script-aided bulk change.
This commit is contained in:
Lars-Dominik Braun
parent
9262c14d73
commit
49a320aaa6
21 changed files with 6891 additions and 6525 deletions
|
|
@ -14823,110 +14823,121 @@ datasets.")
|
|||
(define-public ngless
|
||||
(package
|
||||
(name "ngless")
|
||||
(version "1.3.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ngless-toolkit/ngless.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pb9f6b0yk9p4cdwiym8r190q1bcdiwvc7i2s6rw54qgi8r3g6pj"))
|
||||
(patches (search-patches "ngless-unliftio.patch"))))
|
||||
(version "1.5.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (hackage-uri "NGLess" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pljyrlpr9r3cl5311dhgxdl8y40szyi4vprn34i3piy0qrldymi"))))
|
||||
(build-system haskell-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#: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-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")))
|
||||
(add-after 'create-Versions.hs 'create-cabal-file
|
||||
(lambda _ (invoke "hpack")))
|
||||
;; These tools are expected to be installed alongside ngless.
|
||||
(add-after 'install 'link-tools
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((bin (string-append #$output "/bin/")))
|
||||
(symlink (search-input-file inputs "/bin/prodigal")
|
||||
(string-append bin "ngless-" #$version "-prodigal"))
|
||||
(symlink (search-input-file inputs "/bin/minimap2")
|
||||
(string-append bin "ngless-" #$version "-minimap2"))
|
||||
(symlink (search-input-file inputs "/bin/samtools")
|
||||
(string-append bin "ngless-" #$version "-samtools"))
|
||||
(symlink (search-input-file inputs "/bin/bwa")
|
||||
(string-append bin "ngless-" #$version "-bwa"))))))))
|
||||
(inputs
|
||||
(list prodigal
|
||||
bwa
|
||||
samtools
|
||||
minimap2
|
||||
ghc-aeson
|
||||
ghc-ansi-terminal
|
||||
ghc-async
|
||||
ghc-atomic-write
|
||||
ghc-bytestring-lexing
|
||||
ghc-conduit
|
||||
ghc-conduit-algorithms
|
||||
ghc-conduit-extra
|
||||
ghc-configurator
|
||||
ghc-convertible
|
||||
ghc-data-default
|
||||
ghc-diagrams-core
|
||||
ghc-diagrams-lib
|
||||
ghc-diagrams-svg
|
||||
ghc-double-conversion
|
||||
ghc-edit-distance
|
||||
ghc-either
|
||||
ghc-errors
|
||||
ghc-extra
|
||||
ghc-filemanip
|
||||
ghc-file-embed
|
||||
ghc-gitrev
|
||||
ghc-hashtables
|
||||
ghc-http-conduit
|
||||
ghc-inline-c
|
||||
ghc-inline-c-cpp
|
||||
ghc-int-interval-map
|
||||
ghc-missingh
|
||||
ghc-optparse-applicative
|
||||
ghc-regex
|
||||
ghc-safe
|
||||
ghc-safeio
|
||||
ghc-strict
|
||||
ghc-tar
|
||||
ghc-tar-conduit
|
||||
ghc-unliftio
|
||||
ghc-unliftio-core
|
||||
ghc-vector
|
||||
ghc-yaml
|
||||
ghc-zlib))
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'configure 'update-constraints
|
||||
(lambda _
|
||||
(substitute* "NGLess.cabal"
|
||||
(("\\b(base)\\s+[^,]+" all dep)
|
||||
dep))))
|
||||
(add-after 'unpack 'create-Versions.hs
|
||||
(lambda _
|
||||
(substitute* "NGLess/Dependencies/Versions.hs"
|
||||
(("bwaVersion = .+")
|
||||
(string-append "bwaVersion = \""
|
||||
,(package-version bwa) "\""))
|
||||
(("samtoolsVersion = .+")
|
||||
(string-append "samtoolsVersion = \""
|
||||
,(package-version samtools) "\""))
|
||||
(("prodigalVersion = .+")
|
||||
(string-append "prodigalVersion = \""
|
||||
,(package-version prodigal) "\""))
|
||||
(("megahitVersion = .+")
|
||||
(string-append "megahitVersion = \""
|
||||
,(package-version megahit) "\""))
|
||||
(("minimap2Version = .+")
|
||||
(string-append "minimap2Version = \""
|
||||
,(package-version minimap2) "\"")))))
|
||||
;; See NGLess/FileManagement.hs.
|
||||
(add-after 'install 'wrap-program
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bwa (search-input-file inputs "/bin/bwa"))
|
||||
(samtools (search-input-file inputs "/bin/samtools"))
|
||||
(prodigal (search-input-file inputs "/bin/prodigal"))
|
||||
(minimap2 (search-input-file inputs "/bin/minimap2"))
|
||||
(megahit (search-input-file inputs "/bin/megahit")))
|
||||
(wrap-program (string-append out "/bin/ngless")
|
||||
`("NGLESS_BWA_BIN" " " = (,bwa))
|
||||
`("NGLESS_SAMTOOLS_BIN" " " = (,samtools))
|
||||
`("NGLESS_PRODIGAL_BIN" " " = (,prodigal))
|
||||
`("NGLESS_MINIMAP2_BIN" " " = (,minimap2))
|
||||
`("NGLESS_MEGAHIT_BIN" " " = (,megahit))))))
|
||||
;; Sanity check.
|
||||
(add-after 'wrap-program 'check-install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((ngless (string-append (assoc-ref outputs "out") "/bin/ngless")))
|
||||
(invoke ngless "--check-install")))))))
|
||||
(inputs (list prodigal
|
||||
bwa
|
||||
samtools
|
||||
minimap2
|
||||
megahit
|
||||
ghc-missingh
|
||||
ghc-aeson
|
||||
ghc-ansi-terminal
|
||||
ghc-async
|
||||
ghc-atomic-write
|
||||
ghc-bytestring-lexing
|
||||
ghc-conduit
|
||||
ghc-conduit-algorithms
|
||||
ghc-conduit-extra
|
||||
ghc-configurator
|
||||
ghc-convertible
|
||||
ghc-data-default
|
||||
ghc-edit-distance
|
||||
ghc-either
|
||||
ghc-errors
|
||||
ghc-extra
|
||||
ghc-file-embed
|
||||
ghc-filemanip
|
||||
ghc-hashable
|
||||
ghc-hashtables
|
||||
ghc-hostname
|
||||
ghc-http-client
|
||||
ghc-http-conduit
|
||||
ghc-inline-c
|
||||
ghc-inline-c-cpp
|
||||
ghc-int-interval-map
|
||||
ghc-network
|
||||
ghc-optparse-applicative
|
||||
ghc-primitive
|
||||
ghc-random-shuffle
|
||||
ghc-regex
|
||||
ghc-resourcet
|
||||
ghc-safe
|
||||
ghc-stm-chans
|
||||
ghc-stm-conduit
|
||||
ghc-strict
|
||||
ghc-tar
|
||||
ghc-tar-conduit
|
||||
ghc-unix-compat
|
||||
ghc-unliftio
|
||||
ghc-unliftio-core
|
||||
ghc-vector
|
||||
ghc-vector-algorithms
|
||||
ghc-yaml
|
||||
ghc-zlib
|
||||
ghc-bzlib-conduit
|
||||
ghc-double-conversion
|
||||
ghc-safeio))
|
||||
(propagated-inputs
|
||||
(list r-r6 r-hdf5r r-iterators r-itertools r-matrix))
|
||||
(native-inputs
|
||||
(list ghc-hpack
|
||||
ghc-quickcheck
|
||||
ghc-test-framework
|
||||
ghc-test-framework-hunit
|
||||
ghc-test-framework-quickcheck2
|
||||
ghc-test-framework-th))
|
||||
(native-inputs (list ghc-hunit
|
||||
ghc-quickcheck
|
||||
ghc-tasty
|
||||
ghc-tasty-hunit
|
||||
ghc-tasty-quickcheck
|
||||
ghc-tasty-th))
|
||||
(home-page "https://ngless.embl.de/")
|
||||
(synopsis "DSL for processing next-generation sequencing data")
|
||||
(description "Ngless is a domain-specific language for
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue