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authorEfraim Flashner <efraim@flashner.co.il>2021-01-14 11:26:46 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-14 20:43:31 +0200
commitdb30d6eada7ef0f2a6d41c71f37ed3e45899e414 (patch)
tree215887656d9632305cf02b7a1bc73171e6106490 /gnu
parent2051be4f4cd526fb445e826d655afa40f8f4a7e5 (diff)
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.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm67
1 files changed, 12 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 84a9a4d208..77150e0dce 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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.")
(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
(package
(name "sambamba")
- (version "0.7.1")
+ (version "0.8.0")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lomereiter/sambamba")
+ (url "https://github.com/biod/sambamba")
(commit (string-append "v" version))))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis"))))
+ "07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there is no test target
@@ -10557,52 +10536,30 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(delete 'configure)
(add-after 'unpack 'fix-ldc-version
(lambda _
- (substitute* "gen_ldc_version_info.py"
- (("/usr/bin/env.*") (which "python3")))
(substitute* "Makefile"
;; We use ldc2 instead of ldmd2 to compile sambamba.
(("\\$\\(shell which ldmd2\\)") (which "ldc2")))
#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
(lambda _
(substitute* "Makefile"
- (("htslib/libhts.a lz4/lib/liblz4.a")
- "-L-lhts -L-llz4")
- ((" lz4-static htslib-static") ""))
+ (("= lz4/lib/liblz4.a") "= -L-llz4")
+ (("ldc_version_info lz4-static") "ldc_version_info"))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(copy-file (string-append "bin/sambamba-" ,version)
(string-append bin "/sambamba"))
#t))))))
(native-inputs
- `(("ldc" ,ldc)
- ("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")))))))
+ `(("python" ,python)))
(inputs
- `(("lz4" ,lz4)
- ("htslib" ,htslib-for-sambamba)))
- (home-page "https://lomereiter.github.io/sambamba/")
+ `(("ldc" ,ldc)
+ ("lz4" ,lz4)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/biod/sambamba")
(synopsis "Tools for working with SAM/BAM data")
(description "Sambamba is a high performance modern robust and
fast tool (and library), written in the D programming language, for