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gn: Add pangenie.

wip-tensorflow
Efraim Flashner 11 months ago
parent
commit
4de2b7e3fa
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 48
      gn/packages/bioinformatics.scm

48
gn/packages/bioinformatics.scm

@ -497,6 +497,54 @@ reads.")
collapses them into a non-redundant graph structure.")
(license license:expat)))
(define-public pangenie
(let ((commit "1f3d2d247702e8c90620b8b1c5f6ea866c9aab19") ; April 30, 2021
(revision "1"))
(package
(name "pangenie")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://bitbucket.org/jana_ebler/pangenie.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0qp15dfngg37lk64yn2q8kglkazdwi1vpfr2r783bcx5pywr4n5w"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list (string-append "-DCMAKE_BUILD_RPATH="
(assoc-ref %outputs "out") "/lib"))
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "make" "-C" "tests"))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-directory-excursion "src"
(install-file "PanGenie" (string-append out "/bin"))
(install-file "PanGenie-graph" (string-append out "/bin"))
(install-file "libPanGenieLib.so" (string-append out "/lib"))
)
#t))))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("jellyfish" ,jellyfish)))
(home-page "https://bitbucket.org/jana_ebler")
(synopsis "Genotyping based on k-mers and pangenome graphs")
(description
"This package provides a genotyper for various types of genetic variants
(such as SNPs, indels and structural variants). Genotypes are computed based on
read k-mer counts and a panel of known haplotypes. A description of the method
can be found @url{https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1,
here}.")
(license license:expat))))
;; TODO: Unbundle zlib, bamtools, tclap
(define-public sniffles
(package

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