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authorRicardo Wurmus <rekado@elephly.net>2018-06-14 13:50:21 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-06-14 13:51:15 +0200
commit53131eab2d97a5a2ce43b6f0c7fe47536dbcca84 (patch)
treec4cbb5de527bbe96fb769b7f56c9d74ae82dbb81
parentce573b1128ce0a812d11b66de9f64b393e0a5f50 (diff)
downloadpatches-53131eab2d97a5a2ce43b6f0c7fe47536dbcca84.tar
patches-53131eab2d97a5a2ce43b6f0c7fe47536dbcca84.tar.gz
gnu: Add minimap2.
* gnu/packages/bioinformatics.scm (minimap2): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm59
1 files changed, 59 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 56fae09d93..a210319243 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13247,3 +13247,62 @@ rate speciation and extinction.")
junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This
version does count multisplits.")
(license license:gpl3+))))
+
+(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 "https://lh3.github.io/minimap2/")
+ (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
+ (description "Minimap2 is a versatile sequence alignment program that
+aligns DNA or mRNA sequences against a large reference database. Typical use
+cases include:
+
+@enumerate
+@item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
+@item finding overlaps between long reads with error rate up to ~15%;
+@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
+ reads against a reference genome;
+@item aligning Illumina single- or paired-end reads;
+@item assembly-to-assembly alignment;
+@item full-genome alignment between two closely related species with
+ divergence below ~15%.
+@end enumerate\n")
+ (license license:expat)))