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gnu: Add minimap2.

* gnu/packages/bioinformatics.scm (minimap2): New variable.
This commit is contained in:
Ricardo Wurmus 2018-06-14 13:50:21 +02:00
parent ce573b1128
commit 53131eab2d
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@ -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)))