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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.
master
Ricardo Wurmus 2017-12-18 11:59:50 +01:00
parent fff9b88439
commit f1a2b1cb20
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GPG Key ID: 197A5888235FACAC
1 changed files with 70 additions and 70 deletions
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@ -9397,38 +9397,30 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0))) (license license:artistic2.0)))
(define-public r-seurat (define-public r-seurat
;; Source releases are only made for new x.0 versions. All newer versions (package
;; are only released as pre-built binaries. At the time of this writing the (name "r-seurat")
;; latest binary release is 1.4.0.12, which is equivalent to this commit. (version "2.1.0")
(let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d") (source (origin
(revision "1")) (method url-fetch)
(package (uri (cran-uri "Seurat" version))
(name "r-seurat") (sha256
(version (string-append "1.4.0.12-" revision "." (string-take commit 7))) (base32
(source (origin "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
(method git-fetch) ;; Delete pre-built jar.
(uri (git-reference (snippet
(url "https://github.com/satijalab/seurat") '(begin (delete-file "inst/java/ModularityOptimizer.jar")
(commit commit))) #t))))
(file-name (string-append name "-" version "-checkout")) (properties `((upstream-name . "Seurat")))
(sha256 (build-system r-build-system)
(base32 (arguments
"101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl")) `(#:phases
;; Delete pre-built jar. (modify-phases %standard-phases
(snippet (add-after 'unpack 'build-jar
'(begin (delete-file "inst/java/ModularityOptimizer.jar") (lambda* (#:key inputs #:allow-other-keys)
#t)))) (let ((classesdir "tmp-classes"))
(build-system r-build-system) (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
(arguments (mkdir classesdir)
`(#:phases (with-output-to-file "manifest"
(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 _ (lambda _
(display "Manifest-Version: 1.0 (display "Manifest-Version: 1.0
Main-Class: ModularityOptimizer\n"))) Main-Class: ModularityOptimizer\n")))
@ -9437,49 +9429,57 @@ Main-Class: ModularityOptimizer\n")))
(zero? (system* "jar" (zero? (system* "jar"
"-cmf" "manifest" "-cmf" "manifest"
"inst/java/ModularityOptimizer.jar" "inst/java/ModularityOptimizer.jar"
"-C" classesdir "."))))))))) "-C" classesdir ".")))))))))
(native-inputs (native-inputs
`(("jdk" ,icedtea "jdk"))) `(("jdk" ,icedtea "jdk")))
(propagated-inputs (propagated-inputs
`(("r-ape" ,r-ape) `(("r-ape" ,r-ape)
("r-caret" ,r-caret) ("r-caret" ,r-caret)
("r-cowplot" ,r-cowplot) ("r-cowplot" ,r-cowplot)
("r-dplyr" ,r-dplyr) ("r-diffusionmap" ,r-diffusionmap)
("r-fastica" ,r-fastica) ("r-dplyr" ,r-dplyr)
("r-fnn" ,r-fnn) ("r-dtw" ,r-dtw)
("r-fpc" ,r-fpc) ("r-fnn" ,r-fnn)
("r-gdata" ,r-gdata) ("r-fpc" ,r-fpc)
("r-ggplot2" ,r-ggplot2) ("r-gdata" ,r-gdata)
("r-gplots" ,r-gplots) ("r-ggjoy" ,r-ggjoy)
("r-gridextra" ,r-gridextra) ("r-ggplot2" ,r-ggplot2)
("r-igraph" ,r-igraph) ("r-gplots" ,r-gplots)
("r-irlba" ,r-irlba) ("r-gridextra" ,r-gridextra)
("r-lars" ,r-lars) ("r-hmisc" ,r-hmisc)
("r-mixtools" ,r-mixtools) ("r-ica" ,r-ica)
("r-pbapply" ,r-pbapply) ("r-igraph" ,r-igraph)
("r-plyr" ,r-plyr) ("r-irlba" ,r-irlba)
("r-ranger" ,r-ranger) ("r-lars" ,r-lars)
("r-rcolorbrewer" ,r-rcolorbrewer) ("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp) ("r-matrix" ,r-matrix)
("r-rcppeigen" ,r-rcppeigen) ("r-mixtools" ,r-mixtools)
("r-rcppprogress" ,r-rcppprogress) ("r-nmf" ,r-nmf)
("r-reshape2" ,r-reshape2) ("r-pbapply" ,r-pbapply)
("r-rocr" ,r-rocr) ("r-plotly" ,r-plotly)
("r-rtsne" ,r-rtsne) ("r-ranger" ,r-ranger)
("r-stringr" ,r-stringr) ("r-rcolorbrewer" ,r-rcolorbrewer)
("r-tclust" ,r-tclust) ("r-rcpp" ,r-rcpp)
("r-tsne" ,r-tsne) ("r-rcppprogress" ,r-rcppprogress)
("r-vgam" ,r-vgam))) ("r-reshape2" ,r-reshape2)
(home-page "http://www.satijalab.org/seurat") ("r-rocr" ,r-rocr)
(synopsis "Seurat is an R toolkit for single cell genomics") ("r-rtsne" ,r-rtsne)
(description ("r-sdmtools" ,r-sdmtools)
"This package is an R package designed for QC, analysis, and ("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 exploration of single cell RNA-seq data. It easily enables widely-used
analytical techniques, including the identification of highly variable genes, analytical techniques, including the identification of highly variable genes,
dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
algorithms; density clustering, hierarchical clustering, k-means, and the algorithms; density clustering, hierarchical clustering, k-means, and the
discovery of differentially expressed genes and markers.") discovery of differentially expressed genes and markers.")
(license license:gpl3)))) (license license:gpl3)))
(define-public r-aroma-light (define-public r-aroma-light
(package (package