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gnu: sambamba Update to 0.8.0.

* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0.
[source, home-page]: Update to new upstream URI.
[arguments]: Shorten 'fix-ldc-version phase. Remove
'place-biod-and-undead phase. Update 'unbundle-prerequisites and
'insatll phases.
[native-inputs]: Remove rdmd, biod. Move ldc ...
[inputs]: ... to here. Add zlib.
(htslib-for-sambamba): Remove variable.
This commit is contained in:
Efraim Flashner 2021-01-14 11:26:46 +02:00
parent 2051be4f4c
commit db30d6eada
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@ -10513,41 +10513,20 @@ explore and perform basic analysis of single cell sequencing data coming from
droplet sequencing. It has been particularly tailored for Drop-seq.") droplet sequencing. It has been particularly tailored for Drop-seq.")
(license license:gpl3)))) (license license:gpl3))))
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package
(inherit htslib)
(name "htslib-for-sambamba")
(version (string-append "1.3.1-1." (string-take commit 9)))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/lomereiter/htslib")
(commit commit)))
(file-name (string-append "htslib-" version "-checkout"))
(sha256
(base32
"0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
,@(package-native-inputs htslib))))))
(define-public sambamba (define-public sambamba
(package (package
(name "sambamba") (name "sambamba")
(version "0.7.1") (version "0.8.0")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/lomereiter/sambamba") (url "https://github.com/biod/sambamba")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis")))) "07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc"))))
(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
@ -10557,52 +10536,30 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(delete 'configure) (delete 'configure)
(add-after 'unpack 'fix-ldc-version (add-after 'unpack 'fix-ldc-version
(lambda _ (lambda _
(substitute* "gen_ldc_version_info.py"
(("/usr/bin/env.*") (which "python3")))
(substitute* "Makefile" (substitute* "Makefile"
;; We use ldc2 instead of ldmd2 to compile sambamba. ;; We use ldc2 instead of ldmd2 to compile sambamba.
(("\\$\\(shell which ldmd2\\)") (which "ldc2"))) (("\\$\\(shell which ldmd2\\)") (which "ldc2")))
#t)) #t))
(add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
(copy-recursively (assoc-ref inputs "biod") "BioD")
#t))
(add-after 'unpack 'unbundle-prerequisites (add-after 'unpack 'unbundle-prerequisites
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
(("htslib/libhts.a lz4/lib/liblz4.a") (("= lz4/lib/liblz4.a") "= -L-llz4")
"-L-lhts -L-llz4") (("ldc_version_info lz4-static") "ldc_version_info"))
((" lz4-static htslib-static") ""))
#t)) #t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(bin (string-append out "/bin")))
(mkdir-p bin) (mkdir-p bin)
(copy-file (string-append "bin/sambamba-" ,version) (copy-file (string-append "bin/sambamba-" ,version)
(string-append bin "/sambamba")) (string-append bin "/sambamba"))
#t)))))) #t))))))
(native-inputs (native-inputs
`(("ldc" ,ldc) `(("python" ,python)))
("rdmd" ,rdmd)
("python" ,python)
("biod"
,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/biod/BioD")
(commit commit)))
(file-name (string-append "biod-"
(string-take commit 9)
"-checkout"))
(sha256
(base32
"0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm")))))))
(inputs (inputs
`(("lz4" ,lz4) `(("ldc" ,ldc)
("htslib" ,htslib-for-sambamba))) ("lz4" ,lz4)
(home-page "https://lomereiter.github.io/sambamba/") ("zlib" ,zlib)))
(home-page "https://github.com/biod/sambamba")
(synopsis "Tools for working with SAM/BAM data") (synopsis "Tools for working with SAM/BAM data")
(description "Sambamba is a high performance modern robust and (description "Sambamba is a high performance modern robust and
fast tool (and library), written in the D programming language, for fast tool (and library), written in the D programming language, for