diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/cran.scm | 74 |
1 files changed, 74 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ae6215b2d1..26b983067b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14999,3 +14999,77 @@ plots. Patchwork is a package that expands the API to allow for arbitrarily complex composition of plots by providing mathmatical operators for combining multiple plots.") (license license:expat)))) + +(define-public r-liger + (package + (name "r-liger") + (version "0.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MacoskoLab/liger.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file "inst/java/ModularityOptimizer.jar") + #t)))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-java-part + (lambda* (#:key inputs #:allow-other-keys) + (invoke "unzip" (assoc-ref inputs "optimizer-src")) + (for-each (lambda (file) (invoke "javac" file)) + (find-files "." "\\.java$")) + (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" + (find-files "." "\\.class$")) + #t))))) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-hmisc" ,r-hmisc) + ("r-ica" ,r-ica) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-mclust" ,r-mclust) + ("r-patchwork" ,r-patchwork) + ("r-plyr" ,r-plyr) + ("r-rann-l1" ,r-rann-l1) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-riverplot" ,r-riverplot) + ("r-rtsne" ,r-rtsne) + ("r-snow" ,r-snow))) + (native-inputs + `(("jdk" ,icedtea "jdk") + ;; See https://github.com/MacoskoLab/liger/issues/96 + ;; The optimizer is released under the Expat license. + ("optimizer-src" + ,(origin + (method url-fetch) + (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") + (sha256 + (base32 + "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) + ("unzip" ,unzip) + ("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/MacoskoLab/liger") + (synopsis "Integrate and analyze multiple single-cell datasets") + (description + "LIGER is a package for integrating and analyzing multiple single-cell +datasets, developed and maintained by the Macosko lab. It relies on +integrative non-negative matrix factorization to identify shared and +dataset-specific factors.") + (license license:gpl3))) |