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gnu: Add r-seurat.

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* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
This commit is contained in:
Raoul Jean Pierre Bonnal 2017-01-19 19:55:30 +01:00 committed by Ricardo Wurmus
parent 79849358f8
commit 2441c28414
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1 changed files with 79 additions and 0 deletions
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gnu/packages/bioinformatics.scm
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@ -8609,6 +8609,85 @@ (define-public r-msnid
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