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04/09: gnu: Add bcftools.
From: |
Ben Woodcroft |
Subject: |
04/09: gnu: Add bcftools. |
Date: |
Tue, 27 Sep 2016 10:50:53 +0000 (UTC) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit bdc7be59ebfdce21184ccacb863414d0cbf6fae6
Author: Marius Bakke <address@hidden>
Date: Thu Sep 22 13:47:53 2016 +0100
gnu: Add bcftools.
* gnu/packages/bioinformatics.scm (bcftools): New variable.
---
gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3816c14..e7eb4c0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -265,6 +265,64 @@ instance, it implements several methods to assess
contig-wise read coverage.")
BAM files.")
(license license:expat)))
+(define-public bcftools
+ (package
+ (name "bcftools")
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/bcftools/releases/download/"
+ version "/bcftools-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Delete bundled htslib.
+ '(delete-file-recursively "htslib-1.3.1"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:make-flags
+ (list
+ "USE_GPL=1"
+ (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.a")
+ (string-append "BGZIP=" (assoc-ref %build-inputs "htslib")
"/bin/bgzip")
+ (string-append "TABIX=" (assoc-ref %build-inputs "htslib")
"/bin/tabix"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-Makefile
+ (lambda _
+ (substitute* "Makefile"
+ ;; Do not attempt to build htslib.
+ (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
+ ;; Link against GSL cblas.
+ (("-lcblas") "-lgslcblas"))
+ #t))
+ (delete 'configure)
+ (add-before 'check 'patch-tests
+ (lambda _
+ (substitute* "test/test.pl"
+ (("/bin/bash") (which "bash")))
+ #t)))))
+ (native-inputs
+ `(("htslib" ,htslib)
+ ("perl" ,perl)))
+ (inputs
+ `(("gsl" ,gsl)
+ ("zlib" ,zlib)))
+ (home-page "https://samtools.github.io/bcftools/")
+ (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
+ (description
+ "BCFtools is a set of utilities that manipulate variant calls in the
+Variant Call Format (VCF) and its binary counterpart BCF. All commands work
+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 bedops
(package
(name "bedops")
- branch master updated (8a54c0e -> 99caa6f), Ben Woodcroft, 2016/09/27
- 01/09: gnu: python-pysam: Update to 0.9.1.4., Ben Woodcroft, 2016/09/27
- 06/09: gnu: python-pysam: Delete bundled htslib., Ben Woodcroft, 2016/09/27
- 03/09: gnu: python2-pbcore: Update to 1.2.10., Ben Woodcroft, 2016/09/27
- 09/09: gnu: python-plastid: Update to 1.4.6., Ben Woodcroft, 2016/09/27
- 08/09: gnu: Add python-termcolor., Ben Woodcroft, 2016/09/27
- 07/09: gnu: python-pysam: Enable tests., Ben Woodcroft, 2016/09/27
- 05/09: gnu: python-pysam: Use 'modify-phases'., Ben Woodcroft, 2016/09/27
- 02/09: gnu: Add python-pyxb., Ben Woodcroft, 2016/09/27
- 04/09: gnu: Add bcftools.,
Ben Woodcroft <=