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-rw-r--r--gnu/packages/bioinformatics.scm174
1 files changed, 96 insertions, 78 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fedc8aec4c..cf026ab24e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -421,7 +421,7 @@ computational cluster.")
(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/"
@@ -429,7 +429,7 @@ computational cluster.")
"bedtools-" version ".tar.gz"))
(sha256
(base32
- "0q6fsiz4s52yzxs6h2vxwq95fsi3n64wkpinkk05mfh4dmhybw74"))))
+ "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@@ -466,7 +466,19 @@ BED, GFF/GTF, VCF.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
+ "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
+ (arguments
+ '(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))))))
(define-public ribotaper
(package
@@ -2061,7 +2073,7 @@ identify enrichments with functional annotations of the genome.")
(define-public diamond
(package
(name "diamond")
- (version "0.9.13")
+ (version "0.9.14")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2070,7 +2082,7 @@ identify enrichments with functional annotations of the genome.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pi5ncqwmynqpmmp3j3lhnqrjhj34sr6wpmsgrpkv3wyxx22fv86"))))
+ "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -2905,7 +2917,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
(method url-fetch)
(uri (string-append
"http://eddylab.org/software/hmmer"
- (version-prefix version 1) "/"
+ (version-major version) "/"
version "/hmmer-" version ".tar.gz"))
(sha256
(base32
@@ -9385,83 +9397,89 @@ 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$"))))
- (zero? (system* "jar"
- "-cf" "inst/java/ModularityOptimizer.jar"
- "-C" classesdir ".")))))))))
- (native-inputs
- `(("jdk" ,icedtea "jdk")))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-caret" ,r-caret)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-fastica" ,r-fastica)
- ("r-fnn" ,r-fnn)
- ("r-fpc" ,r-fpc)
- ("r-gdata" ,r-gdata)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gplots" ,r-gplots)
- ("r-gridextra" ,r-gridextra)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-lars" ,r-lars)
- ("r-mixtools" ,r-mixtools)
- ("r-pbapply" ,r-pbapply)
- ("r-plyr" ,r-plyr)
- ("r-ranger" ,r-ranger)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppprogress" ,r-rcppprogress)
- ("r-reshape2" ,r-reshape2)
- ("r-rocr" ,r-rocr)
- ("r-rtsne" ,r-rtsne)
- ("r-stringr" ,r-stringr)
- ("r-tclust" ,r-tclust)
- ("r-tsne" ,r-tsne)
- ("r-vgam" ,r-vgam)))
- (home-page "http://www.satijalab.org/seurat")
- (synopsis "Seurat is an R toolkit for single cell genomics")
- (description
- "This package is an R package designed for QC, analysis, and
+ (package
+ (name "r-seurat")
+ (version "2.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+ ;; Delete pre-built jar.
+ (snippet
+ '(begin (delete-file "inst/java/ModularityOptimizer.jar")
+ #t))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'build-jar
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((classesdir "tmp-classes"))
+ (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+ (mkdir classesdir)
+ (with-output-to-file "manifest"
+ (lambda _
+ (display "Manifest-Version: 1.0
+Main-Class: ModularityOptimizer\n")))
+ (and (zero? (apply system* `("javac" "-d" ,classesdir
+ ,@(find-files "java" "\\.java$"))))
+ (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