@@ 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