diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 140 |
1 files changed, 70 insertions, 70 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99693bd62d..cf026ab24e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9397,38 +9397,30 @@ 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) - - (with-output-to-file "manifest" + (package + (name "r-seurat") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "Seurat" version)) + (sha256 + (base32 + "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x")) + ;; Delete pre-built jar. + (snippet + '(begin (delete-file "inst/java/ModularityOptimizer.jar") + #t)))) + (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"))) @@ -9437,49 +9429,57 @@ Main-Class: ModularityOptimizer\n"))) (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-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 + "-C" classesdir "."))))))))) + (native-inputs + `(("jdk" ,icedtea "jdk"))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-caret" ,r-caret) + ("r-cowplot" ,r-cowplot) + ("r-diffusionmap" ,r-diffusionmap) + ("r-dplyr" ,r-dplyr) + ("r-dtw" ,r-dtw) + ("r-fnn" ,r-fnn) + ("r-fpc" ,r-fpc) + ("r-gdata" ,r-gdata) + ("r-ggjoy" ,r-ggjoy) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-gridextra" ,r-gridextra) + ("r-hmisc" ,r-hmisc) + ("r-ica" ,r-ica) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-lars" ,r-lars) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mixtools" ,r-mixtools) + ("r-nmf" ,r-nmf) + ("r-pbapply" ,r-pbapply) + ("r-plotly" ,r-plotly) + ("r-ranger" ,r-ranger) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppprogress" ,r-rcppprogress) + ("r-reshape2" ,r-reshape2) + ("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))) + (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)))) + (license license:gpl3))) (define-public r-aroma-light (package |