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gnu: r-seurat: Update to 2.3.4.
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4. [source]: Remove snippet. [arguments]: Remove. [native-inputs]: Remove. [propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger, r-stringr, r-tclust, and rvgam; add r-httr.
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1 changed files with 4 additions and 35 deletions
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@ -9701,58 +9701,31 @@ (define-public r-msnid
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(define-public r-seurat
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(package
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(name "r-seurat")
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(version "2.3.2")
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(version "2.3.4")
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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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"1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
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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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"0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
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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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(and (zero? (apply system* `("javac" "-d" ,classesdir
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,@(find-files "java" "\\.java$"))))
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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-cluster" ,r-cluster)
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("r-cowplot" ,r-cowplot)
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("r-diffusionmap" ,r-diffusionmap)
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("r-dosnow" ,r-dosnow)
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("r-dplyr" ,r-dplyr)
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("r-dtw" ,r-dtw)
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("r-fitdistrplus" ,r-fitdistrplus)
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("r-fnn" ,r-fnn)
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("r-foreach" ,r-foreach)
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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-ggridges" ,r-ggridges)
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("r-gplots" ,r-gplots)
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("r-hdf5r" ,r-hdf5r)
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("r-hmisc" ,r-hmisc)
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("r-httr" ,r-httr)
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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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@ -9765,7 +9738,6 @@ (define-public r-seurat
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("r-pbapply" ,r-pbapply)
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("r-plotly" ,r-plotly)
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("r-png" ,r-png)
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("r-ranger" ,r-ranger)
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("r-rann" ,r-rann)
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("r-rcolorbrewer" ,r-rcolorbrewer)
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("r-rcpp" ,r-rcpp)
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@ -9776,11 +9748,8 @@ (define-public r-seurat
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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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("r-tsne" ,r-tsne)))
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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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