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| -rw-r--r-- | gn/packages/bioinformatics.scm | 48 |
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 |