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