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gnu: sambamba: Update to 0.8.2.

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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2.
[arguments]: Sett CC and D_LD in build phase.
[native-inputs]: Add ld-gold-wrapper and binutils-gold.
This commit is contained in:
Ricardo Wurmus 2022-01-17 08:24:58 +01:00
parent 141adf4d13
commit 4acf325150
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1 changed files with 14 additions and 7 deletions
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gnu/packages/bioinformatics.scm
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@ -8979,7 +8979,7 @@ (define-public r-cellchat
(define-public sambamba (define-public sambamba
(package (package
(name "sambamba") (name "sambamba")
(version "0.8.0") (version "0.8.2")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -8989,7 +8989,7 @@ (define-public sambamba
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc")))) "1zdkd1md5wk4la71p82pbclqqcm55abk23fk087da6186i1bsihl"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; there is no test target `(#:tests? #f ; there is no test target
@ -8997,11 +8997,12 @@ (define-public sambamba
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(add-after 'unpack 'fix-ldc-version (add-after 'unpack 'prepare-build-tools
(lambda _ (lambda* (#:key inputs #:allow-other-keys)
(substitute* "Makefile" (substitute* "Makefile"
;; We use ldc2 instead of ldmd2 to compile sambamba. (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
(("\\$\\(shell which ldmd2\\)") (which "ldc2"))))) (setenv "CC" "gcc")
(setenv "D_LD" (which "ld.gold"))))
(add-after 'unpack 'unbundle-prerequisites (add-after 'unpack 'unbundle-prerequisites
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
@ -9014,7 +9015,13 @@ (define-public sambamba
(copy-file (string-append "bin/sambamba-" ,version) (copy-file (string-append "bin/sambamba-" ,version)
(string-append bin "/sambamba")))))))) (string-append bin "/sambamba"))))))))
(native-inputs (native-inputs
(list python)) `(("ld-gold-wrapper"
;; Importing (gnu packages commencement) would introduce a cycle.
,(module-ref (resolve-interface
'(gnu packages commencement))
'ld-gold-wrapper))
("binutils-gold" ,binutils-gold)
("python" ,python)))
(inputs (inputs
(list ldc lz4 zlib)) (list ldc lz4 zlib))
(home-page "https://github.com/biod/sambamba") (home-page "https://github.com/biod/sambamba")