diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 174 |
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 |