X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/157eb89707740cf06fac366006a2f7479e32c236..44d66cf764df1a5f92e32c101bc88b20b8ac96b1:/gnu/packages/bioinformatics.scm diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c3d239d2a..1837ad0bc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,6 +54,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) + #:use-module (guix deprecation) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) @@ -187,7 +189,7 @@ structure of the predicted RNA.") (method git-fetch) ;; BamM is not available on pypi. (uri (git-reference - (url "https://github.com/Ecogenomics/BamM.git") + (url "https://github.com/Ecogenomics/BamM") (commit version) (recursive? #t))) (file-name (git-file-name name version)) @@ -281,7 +283,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pezmaster31/bamtools.git") + (url "https://github.com/pezmaster31/bamtools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -359,7 +361,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/bedops/bedops.git") + (url "https://github.com/bedops/bedops") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -482,7 +484,7 @@ BED, GFF/GTF, VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/pbbam.git") + (url "https://github.com/PacificBiosciences/pbbam") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -538,7 +540,7 @@ Non-PacBio BAMs will cause exceptions to be thrown.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/blasr_libcpp.git") + (url "https://github.com/PacificBiosciences/blasr_libcpp") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -600,7 +602,7 @@ hdf and alignment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/blasr.git") + (url "https://github.com/PacificBiosciences/blasr") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -691,7 +693,7 @@ provides the Ribotaper pipeline.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ratschlab/RiboDiff.git") + (url "https://github.com/ratschlab/RiboDiff") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -735,7 +737,7 @@ independently with transcriptional regulation.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lh3/bioawk.git") + (url "https://github.com/lh3/bioawk") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -898,7 +900,7 @@ Python.") ;; Use GitHub as source because PyPI distribution does not contain ;; test data: https://github.com/biocore/biom-format/issues/693 (uri (git-reference - (url "https://github.com/biocore/biom-format.git") + (url "https://github.com/biocore/biom-format") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -941,7 +943,9 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) + ;; FIXME: Upgrade to pandas 1.0 when + ;; https://github.com/biocore/biom-format/issues/837 is resolved. + ("python-pandas" ,python-pandas-0.25))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) @@ -1323,15 +1327,15 @@ package provides command line tools using the Bio++ library.") (define-public blast+ (package (name "blast+") - (version "2.7.1") + (version "2.10.1") (source (origin (method url-fetch) (uri (string-append - "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" + "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" version "/ncbi-blast-" version "+-src.tar.gz")) (sha256 (base32 - "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh")) + "11kvrrl0mcwww6530r55hccpg3x3msmhr3051fwnjbq8rzg2j1qi")) (modules '((guix build utils))) (snippet '(begin @@ -1563,7 +1567,7 @@ errors at the end of reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/BenLangmead/bowtie2.git") + (url "https://github.com/BenLangmead/bowtie2") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -1779,7 +1783,7 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pkerpedjiev/bwa-pssm.git") + (url "https://github.com/pkerpedjiev/bwa-pssm") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -1809,7 +1813,7 @@ well as many of the command line options.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/brentp/bwa-meth.git") + (url "https://github.com/brentp/bwa-meth") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -1883,7 +1887,7 @@ multiple sequence alignments.") (method git-fetch) ;; Test data is missing on PyPi. (uri (git-reference - (url "https://github.com/pysam-developers/pysam.git") + (url "https://github.com/pysam-developers/pysam") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2032,7 +2036,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mhammell-laboratory/tetoolkit.git") + (url "https://github.com/mhammell-laboratory/tetoolkit") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2145,49 +2149,43 @@ databases.") (define-public clipper (package (name "clipper") - (version "1.2.1") + (version "2.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/YeoLab/clipper.git") + (url "https://github.com/YeoLab/clipper") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb")) - (modules '((guix build utils))) - (snippet - '(begin - ;; remove unnecessary setup dependency - (substitute* "setup.py" - (("setup_requires = .*") "")) - #t)))) + "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:phases + `(#:phases (modify-phases %standard-phases - ;; This is fixed in upstream commit - ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "clipper/src/readsToWiggle.pyx" - (("^sc.*") "")) - #t))))) + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) (inputs - `(("htseq" ,python2-htseq) - ("python-pybedtools" ,python2-pybedtools) - ("python-cython" ,python2-cython) - ("python-scikit-learn" ,python2-scikit-learn) - ("python-matplotlib" ,python2-matplotlib) - ("python-pandas" ,python2-pandas) - ("python-pysam" ,python2-pysam) - ("python-numpy" ,python2-numpy) - ("python-scipy" ,python2-scipy))) + `(("htseq" ,htseq) + ("python-pybedtools" ,python-pybedtools) + ("python-cython" ,python-cython) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-nose" ,python2-nose) ; for tests - ("python-pytz" ,python2-pytz))) ; for tests + `(("python-setuptools-git" ,python-setuptools-git) + ("python-mock" ,python-mock) ; for tests + ("python-nose" ,python-nose) ; for tests + ("python-pytz" ,python-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description @@ -2406,12 +2404,18 @@ interval trees with associated meta-data. It is primarily used by the (name "python-deeptools") (version "3.4.3") (source (origin - (method url-fetch) - (uri (pypi-uri "deepTools" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/deepTools") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -2421,7 +2425,7 @@ interval trees with associated meta-data. It is primarily used by the ("python-pysam" ,python-pysam) ("python-scipy" ,python-scipy) ("python-deeptoolsintervals" ,python-deeptoolsintervals) - ("python-plotly" ,python-plotly))) + ("python-plotly" ,python-plotly-2.4.1))) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts @@ -2436,6 +2440,8 @@ annotations of the genome.") ;; remainder of the code is licensed under the MIT license. (license (list license:bsd-3 license:expat)))) +(define-deprecated deeptools python-deeptools) + (define-public cutadapt (package (name "cutadapt") @@ -2468,7 +2474,7 @@ other types of unwanted sequence from high-throughput sequencing reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dpryan79/libBigWig.git") + (url "https://github.com/dpryan79/libBigWig") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2548,7 +2554,7 @@ accessing bigWig files.") (method git-fetch) ;; Source from GitHub so that tests are included. (uri (git-reference - (url "https://github.com/jeetsukumaran/DendroPy.git") + (url "https://github.com/jeetsukumaran/DendroPy") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2599,51 +2605,6 @@ trees (phylogenies) and characters.") with Python.") (license license:expat))) -(define-public deeptools - (package - (name "deeptools") - (version "3.1.3") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/deepTools.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This phase fails, but it's not needed. - (delete 'reset-gzip-timestamps)))) - (inputs - `(("python-plotly" ,python-plotly) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig))) - (native-inputs - `(("python-mock" ,python-mock) ;for tests - ("python-nose" ,python-nose) ;for tests - ("python-pytz" ,python-pytz))) ;for tests - (home-page "https://github.com/deeptools/deepTools") - (synopsis "Tools for normalizing and visualizing deep-sequencing data") - (description - "DeepTools addresses the challenge of handling the large amounts of data -that are now routinely generated from DNA sequencing centers. To do so, -deepTools contains useful modules to process the mapped reads data to create -coverage files in standard bedGraph and bigWig file formats. By doing so, -deepTools allows the creation of normalized coverage files or the comparison -between two files (for example, treatment and control). Finally, using such -normalized and standardized files, multiple visualizations can be created to -identify enrichments with functional annotations of the genome.") - (license license:gpl3+))) - (define-public delly (package (name "delly") @@ -2651,7 +2612,7 @@ identify enrichments with functional annotations of the genome.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dellytools/delly.git") + (url "https://github.com/dellytools/delly") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2698,7 +2659,7 @@ accurately delineate genomic rearrangements throughout the genome.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/bbuchfink/diamond.git") + (url "https://github.com/bbuchfink/diamond") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2733,7 +2694,7 @@ data and settings.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/maaskola/discrover.git") + (url "https://github.com/maaskola/discrover") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2806,7 +2767,7 @@ of nucleic acid binding proteins.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") + (url "https://github.com/DReichLab/EIG") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3050,16 +3011,16 @@ dynamic programming or a variety of heuristics.") (define-public express (package (name "express") - (version "1.5.1") + (version "1.5.3") (source (origin - (method url-fetch) - (uri - (string-append - "http://bio.math.berkeley.edu/eXpress/downloads/express-" - version "/express-" version "-src.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/adarob/eXpress") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) + "18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -3076,6 +3037,12 @@ dynamic programming or a variety of heuristics.") (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") (string-append (assoc-ref inputs "bamtools") "/lib")) (("libprotobuf.a") "libprotobuf.so")) + #t)) + (add-after 'unpack 'remove-update-check + (lambda _ + (substitute* "src/main.cpp" + (("#include \"update_check.h\"") "") + (("check_version\\(PACKAGE_VERSION\\);") "")) #t))))) (inputs `(("boost" ,boost) @@ -3099,7 +3066,7 @@ ChIP-Seq, and analysis of metagenomic data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dparks1134/ExpressBetaDiversity.git") + (url "https://github.com/dparks1134/ExpressBetaDiversity") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3226,7 +3193,7 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/seqan/flexbar.git") + (url "https://github.com/seqan/flexbar") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3369,7 +3336,7 @@ genes in incomplete assemblies or complete genomes.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/fxtract.git") + (url "https://github.com/ctSkennerton/fxtract") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3405,7 +3372,7 @@ genes in incomplete assemblies or complete genomes.") ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/util.git") + (url "https://github.com/ctSkennerton/util") (commit util-commit))) (file-name (string-append "ctstennerton-util-" util-commit "-checkout")) @@ -3432,7 +3399,7 @@ comment or quality sections.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/xiangzhou/GEMMA.git") + (url "https://github.com/xiangzhou/GEMMA") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3492,7 +3459,7 @@ association studies (GWAS).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nboley/grit.git") + (url "https://github.com/nboley/grit") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3717,7 +3684,7 @@ from high-throughput sequencing assays.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3767,7 +3734,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -3811,7 +3778,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -3839,7 +3806,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -3918,7 +3885,7 @@ VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -4008,7 +3975,7 @@ VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -4205,7 +4172,7 @@ The main functions of FastQC are: (origin (method git-fetch) (uri (git-reference - (url "https://github.com/OpenGene/fastp.git") + (url "https://github.com/OpenGene/fastp") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4285,7 +4252,7 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nboley/idr.git") + (url "https://github.com/nboley/idr") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -4376,7 +4343,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dib-lab/khmer.git") + (url "https://github.com/dib-lab/khmer") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4484,7 +4451,7 @@ experiments.") ;; The PyPi tarball does not contain tests. (method git-fetch) (uri (git-reference - (url "https://github.com/taoliu/MACS.git") + (url "https://github.com/taoliu/MACS") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4607,7 +4574,7 @@ sequences).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/marbl/mash.git") + (url "https://github.com/marbl/mash") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4746,7 +4713,7 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/minced.git") + (url "https://github.com/ctSkennerton/minced") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -4888,7 +4855,7 @@ program for nucleotide and protein sequences.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/tjunier/newick_utils.git") + (url "https://github.com/tjunier/newick_utils") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -5026,7 +4993,7 @@ the phenotype as it models the data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/cDNA_primer.git") + (url "https://github.com/PacificBiosciences/cDNA_primer") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -5247,7 +5214,7 @@ different command-line tools: (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/hyattpd/Prodigal.git") + (url "https://github.com/hyattpd/Prodigal") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -5396,7 +5363,7 @@ extremely diverse sets of genomes.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/stamatak/standard-RAxML.git") + (url "https://github.com/stamatak/standard-RAxML") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -5437,7 +5404,7 @@ phylogenies.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/deweylab/RSEM.git") + (url "https://github.com/deweylab/RSEM") (commit (string-append "v" version)))) (sha256 (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) @@ -5726,7 +5693,7 @@ viewer.") ;; There are no release tarballs nor tags. (method git-fetch) (uri (git-reference - (url "https://github.com/wanpinglee/MOSAIK.git") + (url "https://github.com/wanpinglee/MOSAIK") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -5772,7 +5739,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/ngs.git") + (url "https://github.com/ncbi/ngs") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -5838,7 +5805,7 @@ simultaneously.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/ncbi-vdb.git") + (url "https://github.com/ncbi/ncbi-vdb") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6010,7 +5977,7 @@ subsequent visualization, annotation and storage of results.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/chrchang/plink-ng.git") + (url "https://github.com/chrchang/plink-ng") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6049,7 +6016,7 @@ subsequent visualization, annotation and storage of results.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/smithlab_cpp.git") + (url "https://github.com/smithlabcode/smithlab_cpp") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -6198,7 +6165,7 @@ sequence itself can be retrieved from these databases.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/sra-tools.git") + (url "https://github.com/ncbi/sra-tools") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6408,7 +6375,7 @@ is one that takes arguments.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lh3/seqtk.git") + (url "https://github.com/lh3/seqtk") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6444,7 +6411,7 @@ optionally compressed by gzip.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/amplab/snap.git") + (url "https://github.com/amplab/snap") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6486,7 +6453,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/biocore/sortmerna.git") + (url "https://github.com/biocore/sortmerna") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6532,7 +6499,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/alexdobin/STAR.git") + (url "https://github.com/alexdobin/STAR") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6760,7 +6727,7 @@ Cuffdiff or Ballgown programs.") ;; The Pypi version does not include tests. (method git-fetch) (uri (git-reference - (url "https://github.com/fhcrc/taxtastic.git") + (url "https://github.com/fhcrc/taxtastic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6885,7 +6852,7 @@ sequence.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/hms-dbmi/scde.git") + (url "https://github.com/hms-dbmi/scde") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -7013,14 +6980,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h")))) + "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7331,7 +7298,7 @@ annotation infrastructure.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/torognes/vsearch.git") + (url "https://github.com/torognes/vsearch") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -7532,13 +7499,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2")))) + "0zcx8gha3x3jc0ra6ii6wwq2vfsmffrrnilknbq8h5xjrl55m6ci")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7716,13 +7683,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.24.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0ab92nq7lvhvhgp512qhiiphpby0b17c666qska6p8a636zzmqiv")))) + "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7813,13 +7780,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.44.1") + (version "3.44.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0l6f6lz1rghj8c5s14ljbnmsrwz27fi6a7g42n15n3d3msvflw36")))) + "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7921,13 +7888,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05")))) + "00pd8lsdppxlmx0l65phw0jhsm0qkwjc4wsdxpvgc31iiz9yslbj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7950,13 +7917,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.44.0") + (version "2.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0ag26q9283p9mfz4zx8qnx1w7b7ilmsb8wyx737z9cqy9a0i57wj")))) + "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8119,13 +8086,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c")))) + "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8232,13 +8199,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8")))) + "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8442,7 +8409,7 @@ reference point and sorted by a user defined feature.") ("r-seqpattern" ,r-seqpattern))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description "This package provides a package for summary and annotation of genomic @@ -8475,7 +8442,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (arguments `(#:substitutable? #f)) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description "This package contains experimental genetic data for use with the @@ -8559,16 +8526,12 @@ two-dimensional genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.20") + (version "0.22-11") (source (origin - (method git-fetch) - ;; Not yet available in cran. - (uri (git-reference - (url "https://github.com/rqtl/qtl2.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0")))) + (method url-fetch) + (uri (cran-uri "qtl2" version)) + (sha256 + (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -8578,11 +8541,12 @@ two-dimensional genome scans.") ("r-rsqlite" ,r-rsqlite) ("r-yaml" ,r-yaml))) (home-page "https://kbroman.org/qtl2/") - (synopsis - "QTL analysis software for high-dimensional data and complex cross designs") + (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description - "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software -R/qtl, to better handle high-dimensional data and complex cross designs.") + "This package provides a set of tools to perform @dfn{Quantitative Trait +Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the +@code{R/qtl} package to better handle high-dimensional data and complex cross +designs. Broman et al. (2018) .") (license license:gpl3))) (define-public r-zlibbioc @@ -8839,7 +8803,7 @@ in SNV base substitution data.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ManuSetty/ChIPKernels.git") + (url "https://github.com/ManuSetty/ChIPKernels") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -8873,7 +8837,7 @@ Sequences.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ManuSetty/SeqGL.git") + (url "https://github.com/ManuSetty/SeqGL") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -8923,13 +8887,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.0") + (version "2.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "097znwl95y2vd6asyqxs62m7binwxqmna7ss0302yl3b0s72skcy")))) + "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -9049,7 +9013,7 @@ tools for sequence analysis into a seamless whole.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/arq5x/bits.git") + (url "https://github.com/arq5x/bits") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -9095,7 +9059,7 @@ intervals (e.g. genes, sequence alignments).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/piranha.git") + (url "https://github.com/smithlabcode/piranha") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -9134,7 +9098,7 @@ intervals (e.g. genes, sequence alignments).") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/smithlab_cpp.git") + (url "https://github.com/smithlabcode/smithlab_cpp") (commit commit))) (file-name (string-append "smithlab_cpp-" commit "-checkout")) (sha256 @@ -9187,7 +9151,7 @@ group or two ChIP groups run under different conditions.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ekg/filevercmp.git") + (url "https://github.com/ekg/filevercmp") (commit commit))) (file-name (git-file-name name commit)) (sha256 @@ -9264,7 +9228,7 @@ common bioinformatics tools.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/vatlab/varianttools.git") + (url "https://github.com/vatlab/varianttools") ;; There is no tag corresponding to version 3.1.2 (commit "813ae4a90d25b69abc8a40f4f70441fe09015249"))) (file-name (git-file-name name version)) @@ -9571,14 +9535,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) + "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm")) (modules '((guix build utils))) (snippet '(begin @@ -9600,7 +9564,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.20.0. + ;; mzR version 2.22.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9611,6 +9575,8 @@ proteomics packages.") ("r-rcpp" ,r-rcpp) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -9625,14 +9591,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) + "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9649,14 +9615,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) + "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9677,14 +9643,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) + "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9713,14 +9679,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) + "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9731,6 +9697,8 @@ and specific in detecting differential transcription.") ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -9743,14 +9711,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) + "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9773,14 +9741,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) + "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9806,6 +9774,8 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-scales" ,r-scales) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -9816,14 +9786,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) + "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9916,14 +9886,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) + "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9943,14 +9913,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9974,14 +9944,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) + "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9998,6 +9968,8 @@ distribution.") ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -10013,20 +9985,23 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.24.0") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) + "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -10037,14 +10012,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) + "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10061,6 +10036,8 @@ Shiny-based display methods for Bioconductor objects.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -10076,14 +10053,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) + "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -10106,20 +10083,22 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) + "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-httr" ,r-httr) ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -10130,14 +10109,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.36.0") + (version "2.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) + "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10160,14 +10139,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) + "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10193,14 +10172,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.2.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) + "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10212,6 +10191,8 @@ provide added flexibility for data combination and manipulation.") ("r-globaloptions" ,r-globaloptions) ("r-png" ,r-png) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -10225,14 +10206,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) + "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10254,14 +10235,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.10.2") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) + "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10280,6 +10261,8 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -10297,14 +10280,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) + "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -10329,14 +10312,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) + "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10371,14 +10354,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) + "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5")))) (build-system r-build-system) (arguments `(#:phases @@ -10418,6 +10401,8 @@ effort and encourages consistency.") ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -10434,14 +10419,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) + "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10458,6 +10443,8 @@ interval to data view, mismatch pileup, and several splicing summaries.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -10469,14 +10456,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) + "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10528,14 +10515,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) + "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10552,6 +10539,8 @@ several related annotation packages.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -10566,14 +10555,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) + "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10586,6 +10575,8 @@ by Ernst and Kellis.") ("r-rsamtools" ,r-rsamtools) ("r-snpstats" ,r-snpstats) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -10598,14 +10589,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) + "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10639,6 +10630,8 @@ defining LD blocks.") ("r-snpstats" ,r-snpstats) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -10652,14 +10645,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3")))) + "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10671,6 +10664,7 @@ family of feature/genome hypotheses.") ("r-biovizbase" ,r-biovizbase) ("r-bsgenome" ,r-bsgenome) ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) @@ -10684,6 +10678,8 @@ family of feature/genome hypotheses.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -10698,14 +10694,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.18.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) + "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10714,11 +10710,13 @@ with your data.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) - ("r-homo-sapiens" ,r-homo-sapiens) + ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -10729,13 +10727,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) + "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10751,19 +10749,21 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) + "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-fdrtool" ,r-fdrtool) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -10775,13 +10775,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10804,14 +10804,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.14.4") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb")))) + "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10834,19 +10834,22 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries - (delete-file-recursively "src/winlib/") + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) @@ -10858,14 +10861,7 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") - "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") - (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") - "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") - (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'") - (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")) + ((" \"%s/libsz.a\"") "")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10882,6 +10878,8 @@ block processing.") "C Compiler: GCC\n")) (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") (string-append "HDF5_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) @@ -10907,7 +10905,8 @@ block processing.") (propagated-inputs `(("hdf5" ,hdf5-1.10))) (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)))) + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -10917,19 +10916,21 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) + "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -10940,14 +10941,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) + "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10955,6 +10956,8 @@ matrices.") `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -10967,13 +10970,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.14.6") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck")))) + "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10987,10 +10990,13 @@ libraries.") ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -11001,14 +11007,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.14.6") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr")))) + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -11022,6 +11028,7 @@ quality control.") ("r-dqrng" ,r-dqrng) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) @@ -11030,6 +11037,8 @@ quality control.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -11041,14 +11050,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) + "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -11060,6 +11069,8 @@ variable and significantly correlated genes.") ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -11110,7 +11121,7 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rajewsky-lab/dropbead.git") + (url "https://github.com/rajewsky-lab/dropbead") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -11140,7 +11151,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/htslib.git") + (url "https://github.com/lomereiter/htslib") (commit commit))) (file-name (string-append "htslib-" version "-checkout")) (sha256 @@ -11159,7 +11170,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/sambamba.git") + (url "https://github.com/lomereiter/sambamba") (commit (string-append "v" version)))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -11208,7 +11219,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/biod/BioD.git") + (url "https://github.com/biod/BioD") (commit commit))) (file-name (string-append "biod-" (string-take commit 9) @@ -11235,7 +11246,7 @@ sort, markdup, and depth.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/KlugerLab/Ritornello.git") + (url "https://github.com/KlugerLab/Ritornello") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11281,7 +11292,7 @@ with narrow binding events such as transcription factor ChIP-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/FelixKrueger/TrimGalore.git") + (url "https://github.com/FelixKrueger/TrimGalore") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -11496,7 +11507,7 @@ applications for tackling some common problems in a user-friendly way.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/3DGenomes/TADbit.git") + (url "https://github.com/3DGenomes/TADbit") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11558,7 +11569,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ENCODE-DCC/kentUtils.git") + (url "https://github.com/ENCODE-DCC/kentUtils") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11674,7 +11685,7 @@ browser.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/aboyle/F-seq.git") + (url "https://github.com/aboyle/F-seq") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -11732,7 +11743,7 @@ Browser.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/FelixKrueger/Bismark.git") + (url "https://github.com/FelixKrueger/Bismark") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -11845,6 +11856,9 @@ straight away. Its main features are: (snippet '(begin (for-each delete-file (find-files "." "\\.exe$")) + ;; Some files in the original tarball have restrictive + ;; permissions, which makes repackaging fail + (for-each (lambda (file) (chmod file #o644)) (find-files ".")) #t)))) (build-system gnu-build-system) (arguments @@ -11884,7 +11898,7 @@ using nucleotide or amino-acid sequence data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pachterlab/kallisto.git") + (url "https://github.com/pachterlab/kallisto") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11933,7 +11947,7 @@ accurate as existing quantification tools.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/Kingsford-Group/libgff.git") + (url "https://github.com/Kingsford-Group/libgff") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11956,7 +11970,7 @@ dependency like SeqAn.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/kingsfordgroup/sailfish.git") + (url "https://github.com/kingsfordgroup/sailfish") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -12071,7 +12085,7 @@ dependency like SeqAn.") ("rapmap" ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/RapMap.git") + (url "https://github.com/COMBINE-lab/RapMap") (commit (string-append "sf-v" version)))) (file-name (string-append "rapmap-sf-v" version "-checkout")) (sha256 @@ -12106,7 +12120,7 @@ file(s) containing your reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/staden-io_lib.git") + (url "https://github.com/COMBINE-lab/staden-io_lib") (commit (string-append "v" version)))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -12147,7 +12161,7 @@ The following file formats are supported: (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/salmon.git") + (url "https://github.com/COMBINE-lab/salmon") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -12260,7 +12274,7 @@ The following file formats are supported: ("rapmap" ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/RapMap.git") + (url "https://github.com/COMBINE-lab/RapMap") (commit (string-append "salmon-v" version)))) (file-name (string-append "rapmap-salmon-v" version "-checkout")) (sha256 @@ -12293,7 +12307,7 @@ variational inference.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/linnarsson-lab/loompy.git") + (url "https://github.com/linnarsson-lab/loompy") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -12336,7 +12350,7 @@ single-cell RNA-seq data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/cmzmasek/forester.git") + (url "https://github.com/cmzmasek/forester") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -12542,7 +12556,7 @@ reading, writing, and exporting phylogenetic trees.") (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Core libraries of Java framework for processing biological data") (description "BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical @@ -12585,7 +12599,7 @@ This package provides the core libraries.") (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) @@ -12622,7 +12636,7 @@ forester phylogenomics library for constructing phylogenetic trees."))) (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that contains @@ -12679,7 +12693,7 @@ contains (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) @@ -12716,7 +12730,7 @@ forester phylogenomics library for constructing phylogenetic trees."))) (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that contains @@ -12928,7 +12942,7 @@ once. This package provides tools to perform Drop-seq analyses.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for RNA sequencing experiments") (description "PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high @@ -12997,7 +13011,7 @@ expression report comparing samples in an easily configurable manner.") ("kentutils" ,kentutils))) (native-inputs `(("python-pytest" ,python-pytest))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak calling and reporting for ChIP sequencing experiments. It is easy to use and @@ -13059,7 +13073,7 @@ in an easily configurable manner.") ("trim-galore" ,trim-galore) ("cutadapt" ,cutadapt) ("samtools" ,samtools))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") (description "PiGx BSseq is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation @@ -13123,7 +13137,7 @@ methylation and segmentation.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-yaml" ,r-yaml))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") (description "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are @@ -13152,7 +13166,7 @@ based methods.") ("pigx-chipseq" ,pigx-chipseq) ("pigx-rnaseq" ,pigx-rnaseq) ("pigx-scrnaseq" ,pigx-scrnaseq))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipelines for genomics") (description "PiGx is a collection of genomics pipelines. It includes the following pipelines: @@ -13176,7 +13190,7 @@ HTML reports with interesting findings about your samples.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jsh58/Genrich.git") + (url "https://github.com/jsh58/Genrich") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -13211,7 +13225,7 @@ enrichment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/splatlab/mantis.git") + (url "https://github.com/splatlab/mantis") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13278,7 +13292,7 @@ rate speciation and extinction.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pervouchine/sjcount-full.git") + (url "https://github.com/pervouchine/sjcount-full") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -13383,14 +13397,14 @@ cases include: (name "miniasm") (version "0.3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/lh3/miniasm/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/lh3/miniasm") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 - "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v")))) + (base32 + "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -13403,7 +13417,8 @@ cases include: (lambda* (#:key inputs outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "miniasm" bin) - (install-file "minidot" bin))))))) + (install-file "minidot" bin) + #t)))))) (home-page "https://github.com/lh3/miniasm") (synopsis "Ultrafast de novo assembly for long noisy reads") (description "Miniasm is a very fast OLC-based de novo assembler for noisy @@ -13422,7 +13437,7 @@ Thus the per-base error rate is similar to the raw input reads.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/BIMSBbioinfo/ciRcus.git") + (url "https://github.com/BIMSBbioinfo/ciRcus") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -13468,7 +13483,7 @@ can be calculated, and a number of descriptive plots easily generated.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/gpertea/gffread.git") + (url "https://github.com/gpertea/gffread") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13502,7 +13517,7 @@ can be calculated, and a number of descriptive plots easily generated.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/gpertea/gclib.git") + (url "https://github.com/gpertea/gclib") (commit commit))) (file-name (git-file-name "gclib" version)) (sha256 @@ -13529,7 +13544,7 @@ conversions, region filtering, FASTA sequence extraction and more.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/marvin-jens/find_circ.git") + (url "https://github.com/marvin-jens/find_circ") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13809,7 +13824,7 @@ bound.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/4dn-dcic/pairix.git") + (url "https://github.com/4dn-dcic/pairix") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -13908,7 +13923,7 @@ such as Hi-C contact matrices.") ;; Version 12 is not available on pypi. (method git-fetch) (uri (git-reference - (url "https://github.com/deeptools/HiCMatrix.git") + (url "https://github.com/deeptools/HiCMatrix") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -13948,7 +13963,7 @@ the HiCExplorer and pyGenomeTracks packages.") ;; The latest version is not available on Pypi. (method git-fetch) (uri (git-reference - (url "https://github.com/deeptools/HiCExplorer.git") + (url "https://github.com/deeptools/HiCExplorer") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -14097,7 +14112,7 @@ sequencing data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/renozao/xbioc.git") + (url "https://github.com/renozao/xbioc") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14130,7 +14145,7 @@ provided by Bioconductor packages.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/shenorrLab/csSAM.git") + (url "https://github.com/shenorrLab/csSAM") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14161,7 +14176,7 @@ SAM.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/shenorrLab/bseqsc.git") + (url "https://github.com/shenorrLab/bseqsc") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14209,7 +14224,7 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016) (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rrwick/Porechop.git") + (url "https://github.com/rrwick/Porechop") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14240,7 +14255,7 @@ Barcoding Kit or Rapid Barcoding Kit.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/arq5x/poretools.git") + (url "https://github.com/arq5x/poretools") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14301,7 +14316,7 @@ absolute GSEA.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mahmoudibrahim/JAMM.git") + (url "https://github.com/mahmoudibrahim/JAMM") (commit (string-append "JAMMv" version)))) (file-name (git-file-name name version)) (sha256 @@ -14501,7 +14516,7 @@ datasets.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rrwick/Filtlong.git") + (url "https://github.com/rrwick/Filtlong") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14562,7 +14577,7 @@ choosing which reads pass the filter.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jts/nanopolish.git") + (url "https://github.com/jts/nanopolish") (commit commit) (recursive? #t))) (file-name (git-file-name name version)) @@ -14636,7 +14651,7 @@ polymorphisms) and indels with respect to a reference genome and more.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/etal/cnvkit.git") + (url "https://github.com/etal/cnvkit") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -14672,7 +14687,7 @@ Torrent.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/KlugerLab/pyFIt-SNE.git") + (url "https://github.com/KlugerLab/pyFIt-SNE") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -14935,7 +14950,7 @@ tools which build on STAR, Arriba does not require to reduce the (origin (method git-fetch) (uri (git-reference - (url "https://github.com/MikkelSchubert/adapterremoval.git") + (url "https://github.com/MikkelSchubert/adapterremoval") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -14974,7 +14989,7 @@ sequence for paired-ended data, for which this information is not available.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/matsen/pplacer.git") + (url "https://github.com/matsen/pplacer") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -15196,7 +15211,7 @@ on the needs of the user.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ParkerLab/ataqv.git") + (url "https://github.com/ParkerLab/ataqv") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -15237,7 +15252,7 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (origin (method git-fetch) (uri (git-reference - (url "https://github.com/kcha/psiplot.git") + (url "https://github.com/kcha/psiplot") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -15268,7 +15283,7 @@ are generated using @code{ggplot2}.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nanoporetech/ont_fast5_api.git") + (url "https://github.com/nanoporetech/ont_fast5_api") (commit (string-append "release_" version)))) (file-name (git-file-name name version)) (sha256 @@ -15299,7 +15314,7 @@ and reflect the fast5 file schema, and tools to convert between (origin (method git-fetch) (uri (git-reference - (url "https://github.com/phoenixding/tbsp.git") + (url "https://github.com/phoenixding/tbsp") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15611,7 +15626,7 @@ manipulations on VCF files.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ekg/freebayes.git") + (url "https://github.com/ekg/freebayes") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15729,7 +15744,7 @@ length of a short-read sequencing alignment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/GregoryFaust/samblaster.git") + (url "https://github.com/GregoryFaust/samblaster") (commit (string-append "v." version)))) (file-name (git-file-name name version)) (sha256 @@ -15766,7 +15781,7 @@ pairs.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/velocyto-team/velocyto.R.git") + (url "https://github.com/velocyto-team/velocyto.R") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15807,7 +15822,7 @@ patterns.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dpryan79/MethylDackel.git") + (url "https://github.com/dpryan79/MethylDackel") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -15855,7 +15870,7 @@ containing the reference genome as well.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/daler/gffutils.git") + (url "https://github.com/daler/gffutils") (commit commit))) (file-name (git-file-name name version)) (sha256