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03/07: gnu: bcftools: Update to 1.9.
From: |
Ricardo Wurmus |
Subject: |
03/07: gnu: bcftools: Update to 1.9. |
Date: |
Fri, 5 Oct 2018 03:22:09 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit f79b59e3114af8fcd598427655f3ab9512d58164
Author: Ricardo Wurmus <address@hidden>
Date: Thu Oct 4 21:18:34 2018 +0200
gnu: bcftools: Update to 1.9.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
---
gnu/packages/bioinformatics.scm | 27 +++++++++------------------
1 file changed, 9 insertions(+), 18 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 996e373..8a79f66 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -288,34 +288,25 @@ BAM files.")
(define-public bcftools
(package
(name "bcftools")
- (version "1.8")
+ (version "1.9")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/samtools/bcftools/releases/download/"
- version "/bcftools-" version ".tar.bz2"))
+ (uri (string-append "https://github.com/samtools/bcftools/"
+ "releases/download/"
+ version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
+ "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.8")
+ (delete-file-recursively "htslib-1.9")
#t))))
(build-system gnu-build-system)
(arguments
- `(#:test-target "test"
- #:configure-flags (list "--with-htslib=system")
- #:make-flags
- (list
- "USE_GPL=1"
- "LIBS=-lgsl -lgslcblas"
- (string-append "prefix=" (assoc-ref %outputs "out"))
- (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
- (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib")
"/lib/libhts.so")
- (string-append "BGZIP=" (assoc-ref %build-inputs "htslib")
"/bin/bgzip")
- (string-append "TABIX=" (assoc-ref %build-inputs "htslib")
"/bin/tabix")
- (string-append "PACKAGE_VERSION=" ,version))
+ `(#:configure-flags
+ (list "--enable-libgsl")
+ #:test-target "test"
#:phases
(modify-phases %standard-phases
(add-before 'check 'patch-tests
- branch master updated (4a5e2a9 -> a679821), Ricardo Wurmus, 2018/10/05
- 01/07: gnu: htslib: Update to 1.9., Ricardo Wurmus, 2018/10/05
- 02/07: gnu: samtools: Update to 1.9., Ricardo Wurmus, 2018/10/05
- 03/07: gnu: bcftools: Update to 1.9.,
Ricardo Wurmus <=
- 07/07: gnu: samtools-0.1: Adjust to match changes in samtools., Ricardo Wurmus, 2018/10/05
- 06/07: gnu: deeptools: Update to 3.1.2., Ricardo Wurmus, 2018/10/05
- 04/07: gnu: python-plotly: Add python-pandas to inputs., Ricardo Wurmus, 2018/10/05
- 05/07: gnu: python-pysam: Update to 0.15.1., Ricardo Wurmus, 2018/10/05