benwoodcroft pushed a commit to branch master
in repository guix.
commit 4ab1644049ad2d1cf7a997dfa910a4d7d646e49f
Author: Ben Woodcroft <[email protected]>
Date: Thu Apr 6 22:51:26 2017 +1000
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.
---
gnu/packages/bioinformatics.scm | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 97a58a5..f5122a1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4516,7 +4516,7 @@ to the user's query of interest.")
(define-public samtools
(package
(name "samtools")
- (version "1.3.1")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
@@ -4525,7 +4525,7 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
+ "0vzxjm5vkgvzynl7cssm1l560rqs2amdaib1x8sp2ch9b7bxx9xx"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@@ -4533,7 +4533,7 @@ to the user's query of interest.")
(guix build gnu-build-system)
(guix build utils))
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
- #:configure-flags (list "--with-ncurses")
+ #:configure-flags (list "--with-ncurses" "--with-htslib=system")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-tests
@@ -4556,10 +4556,12 @@ to the user's query of interest.")
(scandir "." (lambda (name) (string-match "\\.h$"
name))))
#t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
- (inputs `(("ncurses" ,ncurses)
- ("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))
+ (inputs
+ `(("htslib" ,htslib)
+ ("ncurses" ,ncurses)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("zlib" ,zlib)))
(home-page "http://samtools.sourceforge.net";)
(synopsis "Utilities to efficiently manipulate nucleotide sequence
alignments")
(description
