--- Begin Message ---
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Subject: |
[PATCH] gnu: Add minimap2. |
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Date: |
Thu, 31 May 2018 15:44:23 +0200 |
* gnu/packages/bioinformatics.scm (minimap2): New variable.
---
gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index abea91372..26b135ef7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13185,3 +13185,62 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and
\"BiSSE-ness\" Other included methods
include Markov models of discrete and continuous trait evolution and constant
rate speciation and extinction.")
(license license:gpl2+)))
+
+(define-public minimap2
+ (package
+ (name "minimap2")
+ (version "2.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lh3/minimap2/";
+ "releases/download/v" version "/"
+ "minimap2-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:make-flags
+ (list "CC=gcc"
+ (let ((system ,(or (%current-target-system)
+ (%current-system))))
+ (cond
+ ((string-prefix? "x86_64" system)
+ "all")
+ ((or (string-prefix? "armhf" system)
+ (string-prefix? "aarch64" system))
+ "arm_neon=1")
+ (_ "sse2only=1"))))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (install-file "minimap2" bin)
+ (mkdir-p man)
+ (install-file "minimap2.1" man))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "Pairwise aligner for genomic and spliced nucleotide sequences")
+ (synopsis "https://lh3.github.io/minimap2/";)
+ (description "Minimap2 is a versatile sequence alignment program that
+aligns DNA or mRNA sequences against a large reference database. Typical use
+cases include:
+
address@hidden
address@hidden mapping PacBio or Oxford Nanopore genomic reads to the human
genome;
address@hidden finding overlaps between long reads with error rate up to ~15%;
address@hidden splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or
Direct RNA
+ reads against a reference genome;
address@hidden aligning Illumina single- or paired-end reads;
address@hidden assembly-to-assembly alignment;
address@hidden full-genome alignment between two closely related species with
+ divergence below ~15%.
address@hidden enumerate\n")
+ (license license:expat)))
--
2.16.3
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