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.
This commit is contained in:
Ricardo Wurmus 2018-09-05 14:20:56 +02:00
parent 07bd90ce90
commit 6f6aef80e3
No known key found for this signature in database
GPG key ID: 197A5888235FACAC

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@ -9701,58 +9701,31 @@ (define-public r-msnid
(define-public r-seurat
(package
(name "r-seurat")
(version "2.3.2")
(version "2.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
;; Delete pre-built jar.
(snippet
'(begin (delete-file "inst/java/ModularityOptimizer.jar")
#t))))
"0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
(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")))
(and (zero? (apply system* `("javac" "-d" ,classesdir
,@(find-files "java" "\\.java$"))))
(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-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
("r-diffusionmap" ,r-diffusionmap)
("r-dosnow" ,r-dosnow)
("r-dplyr" ,r-dplyr)
("r-dtw" ,r-dtw)
("r-fitdistrplus" ,r-fitdistrplus)
("r-fnn" ,r-fnn)
("r-foreach" ,r-foreach)
("r-fpc" ,r-fpc)
("r-gdata" ,r-gdata)
("r-ggplot2" ,r-ggplot2)
("r-ggridges" ,r-ggridges)
("r-gplots" ,r-gplots)
("r-hdf5r" ,r-hdf5r)
("r-hmisc" ,r-hmisc)
("r-httr" ,r-httr)
("r-ica" ,r-ica)
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)
@ -9765,7 +9738,6 @@ (define-public r-seurat
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
("r-png" ,r-png)
("r-ranger" ,r-ranger)
("r-rann" ,r-rann)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
@ -9776,11 +9748,8 @@ (define-public r-seurat
("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)))
("r-tsne" ,r-tsne)))
(home-page "http://www.satijalab.org/seurat")
(synopsis "Seurat is an R toolkit for single cell genomics")
(description