diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 211 |
1 files changed, 111 insertions, 100 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5d132749f..2b20191bb3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |