diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 4 insertions, 35 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 01603d2937..c29122b0cf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9701,58 +9701,31 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (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 @@ Main-Class: ModularityOptimizer\n"))) ("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 @@ Main-Class: ModularityOptimizer\n"))) ("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 |