diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 174 |
1 files changed, 117 insertions, 57 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3628d6231a..f89c60b8cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5826,15 +5826,16 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.6.0a") + (version "2.6.0c") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/alexdobin/STAR/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/alexdobin/STAR.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56")) + "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59")) (modules '((guix build utils))) (snippet '(begin @@ -6938,13 +6939,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.48.0") + (version "1.48.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9")))) + "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7082,14 +7083,14 @@ support for default values, positional argument support, etc.") (define-public r-optparse (package (name "r-optparse") - (version "1.4.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) + "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) @@ -7127,13 +7128,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.18.2") + (version "0.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5")))) + "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7586,13 +7587,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf")))) + "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -8528,43 +8529,51 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.3.4") + (version "1.6.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg")))) + "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-testthat" ,r-testthat) + `(("r-testthat" ,r-testthat) ;; During vignette building knitr checks that "pandoc-citeproc" ;; is in the PATH. ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1))) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-org-ce-eg-db" ,r-org-ce-eg-db) - ("r-org-dm-eg-db" ,r-org-dm-eg-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) + ("r-biostrings" ,r-biostrings) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) - ("r-topgo" ,r-topgo) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dbi" ,r-dbi) ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-knitr" ,r-knitr) + ("r-motifrg" ,r-motifrg) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-org-ce-eg-db" ,r-org-ce-eg-db) + ("r-org-dm-eg-db" ,r-org-dm-eg-db) + ("r-org-mm-eg-db" ,r-org-mm-eg-db) ("r-pbapply" ,r-pbapply) + ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) ("r-plotrix" ,r-plotrix) - ("r-motifrg" ,r-motifrg) - ("r-genomation" ,r-genomation) - ("r-genomicfeatures" ,r-genomicfeatures) + ("r-proxy" ,r-proxy) + ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown))) + ("r-rmarkdown" ,r-rmarkdown) + ("r-s4vectors" ,r-s4vectors) + ("r-topgo" ,r-topgo))) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -8576,7 +8585,7 @@ library implementing most of the pipeline's features.") (define-public rcas-web (package (name "rcas-web") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) @@ -8585,7 +8594,7 @@ library implementing most of the pipeline's features.") "/rcas-web-" version ".tar.gz")) (sha256 (base32 - "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm")))) + "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr")))) (build-system gnu-build-system) (arguments `(#:phases @@ -9696,13 +9705,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys")) + "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9746,6 +9755,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) + ("r-hdf5r" ,r-hdf5r) ("r-hmisc" ,r-hmisc) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) @@ -10060,14 +10070,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q")))) + "0qjwz1hzpjnc90jiinjkikfnr0shi72q3zfdjjz7pxydy0mglq8n")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -11439,7 +11449,7 @@ applications for tackling some common problems in a user-friendly way.") ("python2-numpy" ,python2-numpy) ("python2-matplotlib" ,python2-matplotlib) ("python2-pysam" ,python2-pysam))) - (home-page "http://3dgenomes.github.io/TADbit/") + (home-page "https://3dgenomes.github.io/TADbit/") (synopsis "Analyze, model, and explore 3C-based data") (description "TADbit is a complete Python library to deal with all steps to analyze, @@ -12715,7 +12725,7 @@ contains #:phases (modify-phases %standard-phases ;; FIXME: fails with "java.io.FileNotFoundException: - ;; /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar" + ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar" (delete 'generate-jar-indices) ;; All dependencies must be linked to "lib", because that's where ;; they will be searched for when the Class-Path property of the @@ -12896,7 +12906,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.15") + (version "0.0.17") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12904,20 +12914,10 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg")))) + "1c0x5lswvc8v9fw4iynl5rcfs7h7clzp4hqdnl65ia7rk35n4zg9")))) (build-system gnu-build-system) - (arguments - `(#:tests? #f ; parts of the tests rely on access to the network - #:phases - (modify-phases %standard-phases - (add-after 'install 'wrap-executable - ;; Make sure the executable finds all R modules. - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/pigx-chipseq") - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) - `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) - #t))))) + ;; parts of the tests rely on access to the network + (arguments '(#:tests? #f)) (inputs `(("grep" ,grep) ("coreutils" ,coreutils) @@ -12976,7 +12976,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -12984,7 +12984,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y")))) + "0j1dfjk8m1p1h6d5yw63scjlbx56z8gixmbw626w1vcyblg0frmz")))) (build-system gnu-build-system) (arguments `(#:phases @@ -13043,7 +13043,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -13051,7 +13051,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf")))) + "0a73rilv0vnw42d5rsdq205h4f0x8j3jqv998janh4s324c6w2kj")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -13079,6 +13079,7 @@ methylation and segmentation.") ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("python-pandas" ,python-pandas) + ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) @@ -13236,3 +13237,62 @@ rate speciation and extinction.") junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.") (license license:gpl3+)))) + +(define-public minimap2 + (package + (name "minimap2") + (version "2.10") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/lh3/minimap2/" + "releases/download/v" version "/" + "minimap2-" version ".tar.bz2")) + (sha256 + (base32 + "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:make-flags + (list "CC=gcc" + (let ((system ,(or (%current-target-system) + (%current-system)))) + (cond + ((string-prefix? "x86_64" system) + "all") + ((or (string-prefix? "armhf" system) + (string-prefix? "aarch64" system)) + "arm_neon=1") + (_ "sse2only=1")))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (install-file "minimap2" bin) + (mkdir-p man) + (install-file "minimap2.1" man)) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://lh3.github.io/minimap2/") + (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences") + (description "Minimap2 is a versatile sequence alignment program that +aligns DNA or mRNA sequences against a large reference database. Typical use +cases include: + +@enumerate +@item mapping PacBio or Oxford Nanopore genomic reads to the human genome; +@item finding overlaps between long reads with error rate up to ~15%; +@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA + reads against a reference genome; +@item aligning Illumina single- or paired-end reads; +@item assembly-to-assembly alignment; +@item full-genome alignment between two closely related species with + divergence below ~15%. +@end enumerate\n") + (license license:expat))) |