diff options
author | Marius Bakke <mbakke@fastmail.com> | 2016-09-22 13:47:53 +0100 |
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committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-09-27 20:06:00 +1000 |
commit | bdc7be59ebfdce21184ccacb863414d0cbf6fae6 (patch) | |
tree | 075fb959ec5ef46d19a57b1f0440b096f32c7e92 | |
parent | e301bfc886c90acc1a82dc64ff3a15481396f540 (diff) |
gnu: Add bcftools.
* gnu/packages/bioinformatics.scm (bcftools): New variable.
-rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3816c14916..e7eb4c0f26 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") |