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gn: Add minia.

wip-kaleido
Efraim Flashner 2 months ago
parent
commit
8e59af5447
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 40
      gn/packages/bioinformatics.scm

40
gn/packages/bioinformatics.scm

@ -2407,3 +2407,43 @@ To run the bundled rtg-tools software you will also need java. The
@code{icedtea:jdk} output should work nicely.")
(license (list license:expat ; bundled jsoncpp, klib
license:bsd-2))))
;; TODO:
;; Unbundle gatb-core.
(define-public minia
(package
(name "minia")
(version "3.2.6")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/GATB/minia/releases"
"/download/v" version
"/minia-v" version "-Source.tar.gz"))
(sha256
(base32 "03zg1jh0yjw7546kax8xs0zwiqhaiqz044409jc3ss6nj968ay70"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; Tests are expected to be run manually.
#:configure-flags '("-DNO_SSE=ON") ; Can be removed after unbundling gatb-core.
#:phases
(modify-phases %standard-phases
(add-after 'install 'remove-cruft
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-directory-excursion out
(delete-file-recursively "lib")
(delete-file-recursively "test")
(delete-file "bin/h5cc")
(delete-file "LICENSE")
(delete-file "README.md")
#t)))))))
(inputs
`(("zlib" ,zlib)))
(home-page "https://gatb.inria.fr/software/minia")
(synopsis "Short-read assembler based on a de Bruijn graph")
(description "Minia is a short-read assembler based on a de Bruijn graph,
capable of assembling a human genome on a desktop computer in a day. The output
of Minia is a set of contigs. Back when it was released, Minia produced results
of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).")
(license license:agpl3+)))
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