diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 135 |
1 files changed, 71 insertions, 64 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2b4b400c19..84f070f0fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages databases) @@ -1636,7 +1637,7 @@ databases.") (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported (inputs - `(("htseq" ,htseq) + `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) ("python-cython" ,python2-cython) ("python-scikit-learn" ,python2-scikit-learn) @@ -2981,22 +2982,22 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.6.1") + (version "0.9.1") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" - version ".tar.gz")) + (uri (pypi-uri "HTSeq" version)) (sha256 (base32 - "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (native-inputs + `(("python-cython" ,python-cython))) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) (inputs - `(("python-pysam" ,python2-pysam))) + `(("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -3004,6 +3005,9 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public python2-htseq + (package-with-python2 htseq)) + (define-public java-htsjdk (package (name "java-htsjdk") @@ -5757,14 +5761,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5")))) + "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5794,14 +5798,14 @@ distribution.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3")))) + "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5872,14 +5876,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09")))) + "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6384,13 +6388,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9")))) + "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -6406,13 +6410,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi")))) + "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -6500,14 +6504,14 @@ support for default values, positional argument support, etc.") (define-public r-optparse (package (name "r-optparse") - (version "1.3.2") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) + "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) @@ -6523,13 +6527,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28")))) + "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -6572,14 +6576,14 @@ S4Vectors package itself.") (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-6") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) + "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -6597,13 +6601,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.10.0") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n")))) + "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -6649,13 +6653,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3")))) + "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6704,13 +6708,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.22.0") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3")))) + "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6742,13 +6746,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.32.0") + (version "3.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425")))) + "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6826,13 +6830,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.36.0") + (version "2.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m")))) + "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -6848,13 +6852,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27")))) + "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6875,13 +6879,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j")))) + "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -6905,13 +6909,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9")))) + "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -6929,13 +6933,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.44.0") + (version "2.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg")))) + "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6999,13 +7003,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.2.0") + (version "0.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r")))) + "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7029,13 +7033,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.6.0") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw")))) + "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7060,13 +7064,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy")))) + "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7093,13 +7097,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.36.0") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig")))) + "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) (build-system r-build-system) (arguments `(#:phases @@ -7138,13 +7142,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.28.0") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik")))) + "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7817,7 +7821,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.40-8") + (version "1.41-6") (source (origin (method url-fetch) @@ -7825,7 +7829,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) + "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -8067,14 +8071,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.51") + (version "1.60") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) + "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8584,14 +8588,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf")))) + "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -8624,18 +8628,21 @@ number detection tools.") (define-public r-sva (package (name "r-sva") - (version "3.24.0") + (version "3.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362")))) + "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -8651,14 +8658,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "5.9") + (version "6.0") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd")))) + "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) |