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authorMaxim Cournoyer <maxim.cournoyer@gmail.com>2021-12-22 22:06:11 -0500
committerMaxim Cournoyer <maxim.cournoyer@gmail.com>2022-01-10 11:44:46 -0500
commit801d0ed622e0cbb8dc2b3c698cb8c2074bfe7991 (patch)
tree1f0fe1b9ed179a8a4fc57c118134f2c38d97c228 /gnu
parent23fdb5a69c0aede825628221c81a1cb2f8fd02cb (diff)
gnu: bcftools: Update to 1.14.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 24 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32f123a723..3fda31a645 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -373,7 +373,7 @@ single executable called @code{bam}.")
(define-public bcftools
(package
(name "bcftools")
- (version "1.12")
+ (version "1.14")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@@ -381,12 +381,11 @@ single executable called @code{bam}.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
+ "1jqrma16fx8kpvb3c0462dg0asvmiv5yi8myqmc5ddgwi6p8ivxp"))
(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
`(#:configure-flags
@@ -397,8 +396,7 @@ single executable called @code{bam}.")
(add-before 'check 'patch-tests
(lambda _
(substitute* "test/test.pl"
- (("/bin/bash") (which "bash")))
- #t)))))
+ (("/bin/bash") (which "bash"))))))))
(native-inputs
(list htslib perl))
(inputs
@@ -412,9 +410,25 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
(license (list license:gpl3+ license:expat))))
+(define-public bcftools-1.12
+ (package/inherit bcftools
+ (version "1.12")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/samtools/bcftools/"
+ "releases/download/"
+ version "/bcftools-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
+ (modules '((guix build utils)))
+ (snippet '(begin
+ ;; Delete bundled htslib.
+ (delete-file-recursively "htslib-1.12")))))
+ (native-inputs (list htslib-1.12 perl))))
+
(define-public bcftools-1.10
- (package (inherit bcftools)
- (name "bcftools")
+ (package/inherit bcftools
(version "1.10")
(source (origin
(method url-fetch)
@@ -427,11 +441,8 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.10")
- #t))))
- (build-system gnu-build-system)
- (native-inputs
- (list htslib-1.10 perl))))
+ (delete-file-recursively "htslib-1.10")))))
+ (native-inputs (list htslib-1.10 perl))))
(define-public bedops
(package