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Shipped sambamba

gn-stable
pjotrp 3 years ago
parent
commit
0c6ee6e845
1 changed files with 9 additions and 10 deletions
  1. +9
    -10
      gn/packages/bioinformatics.scm

+ 9
- 10
gn/packages/bioinformatics.scm View File

@@ -921,10 +921,10 @@ association studies (GWAS).")
(license license:gpl3))))

(define-public sambamba
(let ((commit "5a33d571339c966477c1f70ed08f64051f7b41c1"))
(let ((commit "91096e78c81162f855b1044a4b2d41895bd27262"))
(package
(name "sambamba")
(version (string-append "0.6.5-" (string-take commit 7)))
(version (string-append "0.6.6-pre1-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -933,15 +933,15 @@ association studies (GWAS).")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"05nlhwjw17igcwiz4pq0r4f8flrqcy4065fhx4nhpc0g65p70mi5"))))
"0d7d0f3ri8qi5r9wq2wy9wzkr1wm68alfsn20q61lqzrfrfwm93k"))))
(build-system gnu-build-system)
(outputs '("out"
"debug")) ;retain debug symbols - note that -O2 is used
"debug"))
(native-inputs
`(("ldc" ,ldc)
("lz4" ,lz4)
("coreutils" ,coreutils) ; for env
("zlib" ,zlib)
("coreutils" ,coreutils) ; for env
("perl" ,perl) ; Needed for htslib
("ruby" ,ruby) ; Needed for htslib
("python" ,python-2) ; Needed for htslib
@@ -963,7 +963,7 @@ association studies (GWAS).")
(uri (git-reference
(url "https://github.com/biod/BioD.git")
(commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")))
(file-name (string-append "biod-src-" (string-take commit 7) ".tar.gz"))
(file-name (string-append "biod-src-" (string-take commit 7) "-checkout"))
(sha256
(base32 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))
(arguments
@@ -980,13 +980,12 @@ association studies (GWAS).")
(and (with-directory-excursion "htslib"
(zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
"--strip-components=1")))
(zero? (system* "rm" "-r" "BioD"))
(zero? (system* "ln" "--symbolic" "--no-target-directory"
(assoc-ref inputs "biod-src") "BioD")))))
;; (zero? (system* "cp" "--recursive" (string-append (assoc-ref inputs "biod-src") "/*") "BioD/")))))
(copy-recursively (assoc-ref inputs "biod-src") "BioD"))))
(replace
'build
(lambda* (#:key inputs make-flags #:allow-other-keys)
(zero? (system* "make" "-f" "Makefile.guix" "sambamba-ldmd2"
(zero? (system* "make" "-f" "Makefile.guix" "guix-debug"
(string-append "LDC_LIB_PATH="
(assoc-ref inputs "ldc")
"/lib")))))


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