gnu: r-seurat: Update to 2.1.0.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.

1 files changed, 70 insertions, 70 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 99693bd62d..cf026ab24e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9397,38 +9397,30 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
 (define-public r-seurat
-  ;; Source releases are only made for new x.0 versions.  All newer versions
-  ;; are only released as pre-built binaries.  At the time of this writing the
-  ;; latest binary release is 1.4.0.12, which is equivalent to this commit.
-  (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d")
-        (revision "1"))
-    (package
-      (name "r-seurat")
-      (version (string-append "1.4.0.12-" revision "." (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/satijalab/seurat")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl"))
-                ;; Delete pre-built jar.
-                (snippet
-                 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
-                         #t))))
-      (build-system r-build-system)
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'build-jar
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((classesdir "tmp-classes"))
-                 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-                 (mkdir classesdir)
-
-                 (with-output-to-file "manifest"
+  (package
+    (name "r-seurat")
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "Seurat" version))
+              (sha256
+               (base32
+                "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+              ;; Delete pre-built jar.
+              (snippet
+               '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+                       #t))))
+    (properties `((upstream-name . "Seurat")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'build-jar
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((classesdir "tmp-classes"))
+               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+               (mkdir classesdir)
+               (with-output-to-file "manifest"
                  (lambda _
                    (display "Manifest-Version: 1.0
 Main-Class: ModularityOptimizer\n")))
@@ -9437,49 +9429,57 @@ Main-Class: ModularityOptimizer\n")))
                     (zero? (system* "jar"
                                     "-cmf" "manifest"
                                     "inst/java/ModularityOptimizer.jar"
-                                    "-C" classesdir ".")))))))))
-      (native-inputs
-       `(("jdk" ,icedtea "jdk")))
-      (propagated-inputs
-       `(("r-ape" ,r-ape)
-         ("r-caret" ,r-caret)
-         ("r-cowplot" ,r-cowplot)
-         ("r-dplyr" ,r-dplyr)
-         ("r-fastica" ,r-fastica)
-         ("r-fnn" ,r-fnn)
-         ("r-fpc" ,r-fpc)
-         ("r-gdata" ,r-gdata)
-         ("r-ggplot2" ,r-ggplot2)
-         ("r-gplots" ,r-gplots)
-         ("r-gridextra" ,r-gridextra)
-         ("r-igraph" ,r-igraph)
-         ("r-irlba" ,r-irlba)
-         ("r-lars" ,r-lars)
-         ("r-mixtools" ,r-mixtools)
-         ("r-pbapply" ,r-pbapply)
-         ("r-plyr" ,r-plyr)
-         ("r-ranger" ,r-ranger)
-         ("r-rcolorbrewer" ,r-rcolorbrewer)
-         ("r-rcpp" ,r-rcpp)
-         ("r-rcppeigen" ,r-rcppeigen)
-         ("r-rcppprogress" ,r-rcppprogress)
-         ("r-reshape2" ,r-reshape2)
-         ("r-rocr" ,r-rocr)
-         ("r-rtsne" ,r-rtsne)
-         ("r-stringr" ,r-stringr)
-         ("r-tclust" ,r-tclust)
-         ("r-tsne" ,r-tsne)
-         ("r-vgam" ,r-vgam)))
-      (home-page "http://www.satijalab.org/seurat")
-      (synopsis "Seurat is an R toolkit for single cell genomics")
-      (description
-       "This package is an R package designed for QC, analysis, and
+                                    "-C" classesdir  ".")))))))))
+    (native-inputs
+     `(("jdk" ,icedtea "jdk")))
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-caret" ,r-caret)
+       ("r-cowplot" ,r-cowplot)
+       ("r-diffusionmap" ,r-diffusionmap)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dtw" ,r-dtw)
+       ("r-fnn" ,r-fnn)
+       ("r-fpc" ,r-fpc)
+       ("r-gdata" ,r-gdata)
+       ("r-ggjoy" ,r-ggjoy)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gplots" ,r-gplots)
+       ("r-gridextra" ,r-gridextra)
+       ("r-hmisc" ,r-hmisc)
+       ("r-ica" ,r-ica)
+       ("r-igraph" ,r-igraph)
+       ("r-irlba" ,r-irlba)
+       ("r-lars" ,r-lars)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-mixtools" ,r-mixtools)
+       ("r-nmf" ,r-nmf)
+       ("r-pbapply" ,r-pbapply)
+       ("r-plotly" ,r-plotly)
+       ("r-ranger" ,r-ranger)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppprogress" ,r-rcppprogress)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rocr" ,r-rocr)
+       ("r-rtsne" ,r-rtsne)
+       ("r-sdmtools" ,r-sdmtools)
+       ("r-stringr" ,r-stringr)
+       ("r-tclust" ,r-tclust)
+       ("r-tidyr" ,r-tidyr)
+       ("r-tsne" ,r-tsne)
+       ("r-vgam" ,r-vgam)))
+    (home-page "http://www.satijalab.org/seurat")
+    (synopsis "Seurat is an R toolkit for single cell genomics")
+    (description
+     "This package is an R package designed for QC, analysis, and
 exploration of single cell RNA-seq data.  It easily enables widely-used
 analytical techniques, including the identification of highly variable genes,
 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
 algorithms; density clustering, hierarchical clustering, k-means, and the
 discovery of differentially expressed genes and markers.")
-      (license license:gpl3))))
+    (license license:gpl3)))
 
 (define-public r-aroma-light
   (package