(define-public bedtools
(package
(name "bedtools")
- (version "2.27.0")
+ (version "2.27.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/releases/"
"bedtools-" version ".tar.gz"))
(sha256
(base32
- "0q6fsiz4s52yzxs6h2vxwq95fsi3n64wkpinkk05mfh4dmhybw74"))))
+ "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
(define-public diamond
(package
(name "diamond")
- (version "0.9.13")
+ (version "0.9.14")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pi5ncqwmynqpmmp3j3lhnqrjhj34sr6wpmsgrpkv3wyxx22fv86"))))
+ "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.4-4")
+ (version "2.4-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "1n57dzv2aid6iqd9fkqik401sidqanhzsawyak94qbiyh6dbd1x9"))))
+ "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.24.1")
+ (version "1.24.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1hwckj4ijgpdchbakvh60nmcaz4fwd5yplhn0880z3dnlsrp8ik3"))))
+ "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.6.0")
+ (version "2.6.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "05f2j9fx8s5gh4f8qkl6wcz32ghz04wxhqb3xxcn1bj24qd7x1x8"))))
+ "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.20.1")
+ (version "3.20.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "01qnxwr9rmz8r5ga3hvjk632365ga2aygx71mxkk7jiad2pjznsp"))))
+ "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.34.2")
+ (version "3.34.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1zyw01z9crm1jc86fva4pqxd9zxfsbsqwjq6ry39gag9pfb7pwcz"))))
+ "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.34.0")
+ (version "2.34.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1dn3ysf0vb3mmg2b3380g0j1ajf88x4rh7fddfp990h2xlnsy2cx"))))
+ "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-httr" ,r-httr)
("r-progress" ,r-progress)
("r-rcurl" ,r-rcurl)
("r-stringr" ,r-stringr)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.38.0")
+ (version "1.38.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "12al1ygzy9p4myxa1fd817m28x2fj6f863znk9bw3hp7knbi98dh"))))
+ "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "1qhxlfl85ifr30wrsidcn3kca3vs8fd8cmwd82gvgx9ppww8vs06"))))
+ "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(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$"))))
- (zero? (system* "jar"
- "-cf" "inst/java/ModularityOptimizer.jar"
- "-C" classesdir ".")))))))))
- (native-inputs
- `(("jdk" ,icedtea "jdk")))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-caret" ,r-caret)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-fastica" ,r-fastica)
- ("r-fnn" ,r-fnn)
- ("r-fpc" ,r-fpc)
- ("r-gdata" ,r-gdata)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gplots" ,r-gplots)
- ("r-gridextra" ,r-gridextra)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-lars" ,r-lars)
- ("r-mixtools" ,r-mixtools)
- ("r-pbapply" ,r-pbapply)
- ("r-plyr" ,r-plyr)
- ("r-ranger" ,r-ranger)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppprogress" ,r-rcppprogress)
- ("r-reshape2" ,r-reshape2)
- ("r-rocr" ,r-rocr)
- ("r-rtsne" ,r-rtsne)
- ("r-stringr" ,r-stringr)
- ("r-tclust" ,r-tclust)
- ("r-tsne" ,r-tsne)
- ("r-vgam" ,r-vgam)))
- (home-page "http://www.satijalab.org/seurat")
- (synopsis "Seurat is an R toolkit for single cell genomics")
- (description
- "This package is an R package designed for QC, analysis, and
+ (package
+ (name "r-seurat")
+ (version "2.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+ ;; Delete pre-built jar.
+ (snippet
+ '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+ #t))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'build-jar
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((classesdir "tmp-classes"))
+ (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+ (mkdir classesdir)
+ (with-output-to-file "manifest"
+ (lambda _
+ (display "Manifest-Version: 1.0
+Main-Class: ModularityOptimizer\n")))
+ (and (zero? (apply system* `("javac" "-d" ,classesdir
+ ,@(find-files "java" "\\.java$"))))
+ (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-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
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
- (version "1.10.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLstats" version))
(sha256
(base32
- "1cbdqawxzgna8rrgj3siph5sw4d2pb57qc0gn6ibfkhyk45f8gdv"))))
+ "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
(properties `((upstream-name . "gQTLstats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.22.0")
+ (version "1.22.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "1lrw65a8426wpxw975wjcaiacpp6fqa00nif1yxigyankbfs23c8"))))
+ "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
HCoop / jackhill / guix / guix.git / blobdiff