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authorEfraim Flashner2021-08-11 10:04:46 +0300
committerEfraim Flashner2021-08-11 10:04:46 +0300
commit4de2b7e3fad083d0ed488662fc624c370d45485a (patch)
tree9867d8effa1a214d34b1e7ee2b55d19e27dc80a9 /gn
parentee9e292453b57efceb0ba5475370ce33cc8fa676 (diff)
downloadguix-bioinformatics-4de2b7e3fad083d0ed488662fc624c370d45485a.tar.gz
gn: Add pangenie.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm48
1 files changed, 48 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index e9893e2..35fadc7 100644
--- a/gn/packages/bioinformatics.scm
+++ b/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