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85/142: gnu: samtools: Update to 1.14.
From: |
guix-commits |
Subject: |
85/142: gnu: samtools: Update to 1.14. |
Date: |
Mon, 10 Jan 2022 13:07:26 -0500 (EST) |
apteryx pushed a commit to branch version-1.4.0
in repository guix.
commit 23fdb5a69c0aede825628221c81a1cb2f8fd02cb
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
AuthorDate: Wed Dec 22 21:37:35 2021 -0500
gnu: samtools: Update to 1.14.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases. This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
---
gnu/packages/bioinformatics.scm | 70 +++++++++++++++++++++++++++--------------
1 file changed, 46 insertions(+), 24 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36167d0ba0..32f123a723 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6144,7 +6144,7 @@ to the user's query of interest.")
(define-public samtools
(package
(name "samtools")
- (version "1.12")
+ (version "1.14")
(source
(origin
(method url-fetch)
@@ -6153,40 +6153,21 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
+ "0x3xdda78ac5vx66b3jdsv9sfhyz4npl4znl1zbaf3lbm6xdlhck"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.12")
- #t))))
+ (delete-file-recursively "htslib-1.14")))))
(build-system gnu-build-system)
(arguments
- `(#:modules ((ice-9 ftw)
- (ice-9 regex)
- (guix build gnu-build-system)
- (guix build utils))
- #:configure-flags (list "--with-ncurses")
+ `(#:configure-flags (list "--with-ncurses")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-tests
(lambda _
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
- (("/bin/bash") (which "bash")))
- #t))
- (add-after 'install 'install-library
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
- (install-file "libbam.a" lib)
- #t)))
- (add-after 'install 'install-headers
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((include (string-append (assoc-ref outputs "out")
- "/include/samtools/")))
- (for-each (lambda (file)
- (install-file file include))
- (scandir "." (lambda (name) (string-match "\\.h$"
name))))
- #t))))))
+ (("/bin/bash") (which "bash"))))))))
(native-inputs (list pkg-config))
(inputs
(list htslib ncurses perl python zlib))
@@ -6199,6 +6180,47 @@ variant calling (in conjunction with bcftools), and a
simple alignment
viewer.")
(license license:expat)))
+(define-public samtools-1.12
+ (package/inherit samtools
+ (version "1.12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/samtools/samtools/"
+ version "/samtools-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
+ (modules '((guix build utils)))
+ (snippet '(begin
+ ;; Delete bundled htslib.
+ (delete-file-recursively "htslib-1.12")))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments samtools)
+ ((#:modules _ #f)
+ '((ice-9 ftw)
+ (ice-9 regex)
+ (guix build gnu-build-system)
+ (guix build utils)))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'install 'install-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+ (install-file "libbam.a" lib))))
+ (add-after 'install 'install-headers
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((include (string-append (assoc-ref outputs "out")
+ "/include/samtools/")))
+ (for-each (lambda (file)
+ (install-file file include))
+ (scandir "." (lambda (name)
+ (string-match "\\.h$" name)))))))))))
+ (native-inputs (list pkg-config))
+ (inputs
+ (list htslib-1.12 ncurses perl python zlib))))
+
(define-public samtools-1.10
(package (inherit samtools)
(name "samtools")
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- 85/142: gnu: samtools: Update to 1.14.,
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