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gnu: samtools: Update to 1.4.1. 

* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
This commit is contained in:
Ben Woodcroft 2017-04-06 22:51:26 +10:00
parent a9e4a1e641
commit 4ab1644049
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1 changed files with 9 additions and 7 deletions
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@ -4516,7 +4516,7 @@ to the user's query of interest.")
(define-public samtools (define-public samtools
(package (package
(name "samtools") (name "samtools")
(version "1.3.1") (version "1.4.1")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -4525,7 +4525,7 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2")) version "/samtools-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc")))) "0vzxjm5vkgvzynl7cssm1l560rqs2amdaib1x8sp2ch9b7bxx9xx"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:modules ((ice-9 ftw) `(#:modules ((ice-9 ftw)
@ -4533,7 +4533,7 @@ to the user's query of interest.")
(guix build gnu-build-system) (guix build gnu-build-system)
(guix build utils)) (guix build utils))
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:configure-flags (list "--with-ncurses") #:configure-flags (list "--with-ncurses" "--with-htslib=system")
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'patch-tests (add-after 'unpack 'patch-tests
@ -4556,10 +4556,12 @@ to the user's query of interest.")
(scandir "." (lambda (name) (string-match "\\.h$" name)))) (scandir "." (lambda (name) (string-match "\\.h$" name))))
#t)))))) #t))))))
(native-inputs `(("pkg-config" ,pkg-config))) (native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses) (inputs
("perl" ,perl) `(("htslib" ,htslib)
("python" ,python) ("ncurses" ,ncurses)
("zlib" ,zlib))) ("perl" ,perl)
("python" ,python)
("zlib" ,zlib)))
(home-page "http://samtools.sourceforge.net") (home-page "http://samtools.sourceforge.net")
(synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
(description (description