@@ 8609,6 8609,85 @@ contains a number of utilities to explore the MS/MS results and assess missed
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)
+ (and (zero? (apply system* `("javac" "-d" ,classesdir
+ ,@(find-files "java" "\\.java$"))))
+ (zero? (system* "jar"
+ "-cf" "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
+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))))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package