rekado pushed a commit to branch master
in repository guix.
commit 86d3822862d655cfef7ee359464288d9953ec2c0
Author: Ricardo Wurmus <rek...@elephly.net>
Date: Thu Aug 15 17:02:49 2019 +0200
gnu: Add r-liger.
* gnu/packages/cran.scm (r-liger): New variable.
---
gnu/packages/cran.scm | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 74 insertions(+)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ae6215b..26b9830 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)))
