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gnu: Update sambamba to 0.7.1.

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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
  Remove unneeded undead input.
This commit is contained in:
Roel Janssen 2020-03-26 18:08:27 +01:00
parent db47adb0c7
commit 79c395dde3
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GPG key ID: CBD0CD5138C19AFC
1 changed files with 6 additions and 19 deletions
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gnu/packages/bioinformatics.scm
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@ -10977,7 +10977,7 @@ (define htslib-for-sambamba
(define-public sambamba
(package
(name "sambamba")
(version "0.6.8")
(version "0.7.1")
(source
(origin
(method git-fetch)
@ -10987,7 +10987,7 @@ (define-public sambamba
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
"111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there is no test target
@ -11006,7 +11006,6 @@ (define-public sambamba
(add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
(copy-recursively (assoc-ref inputs "biod") "BioD")
(copy-recursively (assoc-ref inputs "undead") "undeaD")
#t))
(add-after 'unpack 'unbundle-prerequisites
(lambda _
@ -11020,14 +11019,15 @@ (define-public sambamba
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(mkdir-p bin)
(install-file "bin/sambamba" bin)
(copy-file (string-append "bin/sambamba-" ,version)
(string-append bin "/sambamba"))
#t))))))
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
("python" ,python)
("biod"
,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101"))
(origin
(method git-fetch)
(uri (git-reference
@ -11038,20 +11038,7 @@ (define-public sambamba
"-checkout"))
(sha256
(base32
"1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
("undead"
,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/biod/undeaD.git")
(commit commit)))
(file-name (string-append "undead-"
(string-take commit 9)
"-checkout"))
(sha256
(base32
"1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
"0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm")))))))
(inputs
`(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))