X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/8ab70bae52f8d4b6356ec3b8a88cebf9debe8520..ffe714b5f441ca22d69ecef34bdbb8e61bf758c4:/gnu/packages/bioinformatics.scm diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f60a918d75..ffa2618458 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 @@ -1642,7 +1646,8 @@ gapped, local, and paired-end alignment modes.") (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("tbb" ,tbb) + `(("python-wrapper" ,python-wrapper) + ("tbb" ,tbb) ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) (home-page "http://bowtie-bio.sourceforge.net/index.shtml") @@ -1679,6 +1684,17 @@ genome (2.9 GB for paired-end).") '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases + (add-after 'set-paths 'hide-default-gcc + (lambda* (#:key inputs #:allow-other-keys) + (let ((gcc (assoc-ref inputs "gcc"))) + ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent + ;; conflicts with the GCC 5 input. + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append gcc "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":")) + #t))) (add-after 'unpack 'use-system-samtools (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Makefile.in" @@ -1701,7 +1717,7 @@ genome (2.9 GB for paired-end).") (("#include ") "#include ")) #t))))) (native-inputs - `(("gcc" ,gcc-5))) ;; doesn't build with later versions + `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) @@ -1779,7 +1795,7 @@ 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 +1825,7 @@ 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 +1899,7 @@ 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 +2048,7 @@ 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 +2161,43 @@ 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 +2416,18 @@ 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 +2437,7 @@ 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 +2452,8 @@ 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 +2486,7 @@ 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 +2566,7 @@ 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 @@ -2599,63 +2617,18 @@ 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") - (version "0.7.9") + (version "0.8.3") (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 - (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy")) (modules '((guix build utils))) (snippet '(begin @@ -2679,9 +2652,9 @@ identify enrichments with functional annotations of the genome.") #t)))))) (inputs `(("boost" ,boost) + ("bzip2" ,bzip2) ("htslib" ,htslib) - ("zlib" ,zlib) - ("bzip2" ,bzip2))) + ("zlib" ,zlib))) (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method @@ -2698,7 +2671,7 @@ 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 +2706,7 @@ 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 +2779,7 @@ 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 +3023,16 @@ 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 +3049,12 @@ 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 +3078,7 @@ 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 +3205,7 @@ 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 +3348,7 @@ 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 +3384,7 @@ 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 +3411,7 @@ 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 +3471,7 @@ 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 @@ -3639,7 +3618,7 @@ particular, reads spanning multiple exons.") (native-inputs `(("unzip" ,unzip) ; needed for archive from ftp ("perl" ,perl) - ("pandoc" ,ghc-pandoc))) ; for documentation + ("pandoc" ,pandoc))) ; for documentation (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml") (synopsis "Graph-based alignment of genomic sequencing reads") (description "HISAT2 is a fast and sensitive alignment program for mapping @@ -3717,7 +3696,7 @@ 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 +3746,7 @@ 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 +3790,7 @@ 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 +3818,7 @@ 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 +3897,7 @@ 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 +3987,7 @@ 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 +4184,7 @@ 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 +4264,7 @@ 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 +4355,7 @@ 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 +4463,7 @@ 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 +4586,7 @@ 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 +4725,7 @@ 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 +4867,7 @@ 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 +5005,7 @@ 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 +5226,7 @@ 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 +5375,7 @@ 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 +5416,7 @@ 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 +5705,7 @@ 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 +5751,7 @@ 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 +5817,7 @@ 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 +5989,7 @@ 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 +6028,7 @@ 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 +6177,7 @@ 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 @@ -6378,14 +6357,14 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) + "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) (build-system python-build-system) (inputs `(("python-biopython" ,python-biopython))) @@ -6408,7 +6387,7 @@ 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 +6423,7 @@ 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 +6465,7 @@ 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 +6511,7 @@ 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 +6739,7 @@ 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 +6864,7 @@ 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 +6992,14 @@ 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 +7310,7 @@ 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 +7511,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.56.0") + (version "1.56.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2")))) + "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7716,13 +7695,13 @@ 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 +7792,13 @@ 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 +7900,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.50.0") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05")))) + "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7950,13 +7929,13 @@ 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) @@ -8086,13 +8065,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1lz7a0rrlfv3w44n073mk8pw39z7lfs0njdxp5vpp0rdsmvdf1qk")))) + "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -8119,13 +8098,13 @@ 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 +8211,13 @@ 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 +8421,7 @@ 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 +8454,7 @@ 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 @@ -8531,60 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl - (package - (name "r-qtl") - (version "1.46-2") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/qtl_" - version ".tar.gz")) - (sha256 - (base32 - "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) - (build-system r-build-system) - (home-page "https://rqtl.org/") - (synopsis "R package for analyzing QTL experiments in genetics") - (description "R/qtl is an extension library for the R statistics -system. It is used to analyze experimental crosses for identifying -genes contributing to variation in quantitative traits (so-called -quantitative trait loci, QTLs). - -Using a hidden Markov model, R/qtl estimates genetic maps, to -identify genotyping errors, and to perform single-QTL and two-QTL, -two-dimensional genome scans.") - (license license:gpl3))) - -(define-public r-qtl2 - (package - (name "r-qtl2") - (version "0.20") - (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")))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("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") - (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.") - (license license:gpl3))) - (define-public r-zlibbioc (package (name "r-zlibbioc") @@ -8729,7 +8654,7 @@ paired-end data.") ("r-rtracklayer" ,r-rtracklayer) ("r-rmarkdown" ,r-rmarkdown) ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,ghc-pandoc))) + ("pandoc" ,pandoc))) (native-inputs `(("r-knitr" ,r-knitr))) (synopsis "RNA-centric annotation system") @@ -8839,7 +8764,7 @@ 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 +8798,7 @@ 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 +8848,13 @@ 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 +8974,7 @@ 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 +9020,7 @@ 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 +9059,7 @@ 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 +9112,7 @@ 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 +9189,7 @@ 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)) @@ -9468,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.") (license license:artistic2.0))) -(define-public r-seqminer - (package - (name "r-seqminer") - (version "8.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "seqminer" version)) - (sha256 - (base32 - "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (home-page "http://seqminer.genomic.codes") - (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") - (description - "This package provides tools to integrate nucleotide sequencing -data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") - ;; Any version of the GPL is acceptable - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-raremetals2 (package (name "r-raremetals2") @@ -9522,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-maldiquant - (package - (name "r-maldiquant") - (version "1.19.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "MALDIquant" version)) - (sha256 - (base32 - "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) - (properties `((upstream-name . "MALDIquant"))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/MALDIquant") - (synopsis "Quantitative analysis of mass spectrometry data") - (description - "This package provides a complete analysis pipeline for matrix-assisted -laser desorption/ionization-time-of-flight (MALDI-TOF) and other -two-dimensional mass spectrometry data. In addition to commonly used plotting -and processing methods it includes distinctive features, namely baseline -subtraction methods such as morphological filters (TopHat) or the -statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak -alignment using warping functions, handling of replicated measurements as well -as allowing spectra with different resolutions.") - (license license:gpl3+))) - (define-public r-protgenerics (package (name "r-protgenerics") @@ -9858,67 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) -(define-public r-seurat - (package - (name "r-seurat") - (version "3.1.5") - (source (origin - (method url-fetch) - (uri (cran-uri "Seurat" version)) - (sha256 - (base32 - "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm")))) - (properties `((upstream-name . "Seurat"))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-sctransform" ,r-sctransform) - ("r-tsne" ,r-tsne) - ("r-uwot" ,r-uwot))) - (home-page "http://www.satijalab.org/seurat") - (synopsis "Seurat is an R toolkit for single cell genomics") - (description - "This package is an R package designed for QC, analysis, and -exploration of single cell RNA-seq data. It easily enables widely-used -analytical techniques, including the identification of highly variable genes, -dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering -algorithms; density clustering, hierarchical clustering, k-means, and the -discovery of differentially expressed genes and markers.") - (license license:gpl3))) - (define-public r-aroma-light (package (name "r-aroma-light") @@ -10048,14 +9864,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.20.0") + (version "2.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz")))) + "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10145,17 +9961,18 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.37.0") + (version "2.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr")))) + "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) ("r-graph" ,r-graph) ("r-keggrest" ,r-keggrest))) (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" @@ -10208,14 +10025,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l")))) + "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10840,14 +10657,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1g848s0qc6i4ipd7y2s5pk8k1xggk2kfy0gnr8wjjs2gq3914aw4")))) + "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10870,14 +10687,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "09ylwyk6a8sdrmi1mx7vpycpykqlqylmwa973g6jrcmk0h0qfa4w")) + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) (modules '((guix build utils))) (snippet '(begin @@ -10897,14 +10714,7 @@ 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)) @@ -11013,13 +10823,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0pi4mpc3lvskj5biyhc9cskcnz9q2wjmfrz7xdnx8qqd8vpy84g3")))) + "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -11093,14 +10903,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0i6gw8058gw9yajya3w9qq6l3p634fq9sv8dh8ifigxz0k9b98r6")))) + "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -11126,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) -(define-public r-phangorn - (package - (name "r-phangorn") - (version "2.5.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "phangorn" version)) - (sha256 - (base32 - "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-fastmatch" ,r-fastmatch) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/KlausVigo/phangorn") - (synopsis "Phylogenetic analysis in R") - (description - "Phangorn is a package for phylogenetic analysis in R. It supports -estimation of phylogenetic trees and networks using Maximum Likelihood, -Maximum Parsimony, distance methods and Hadamard conjugation.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -11164,7 +10946,7 @@ 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 @@ -11194,7 +10976,7 @@ 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 @@ -11213,7 +10995,7 @@ 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 @@ -11262,7 +11044,7 @@ 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) @@ -11289,7 +11071,7 @@ 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 @@ -11335,7 +11117,7 @@ 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 @@ -11550,7 +11332,7 @@ 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 @@ -11612,7 +11394,7 @@ 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 @@ -11728,7 +11510,7 @@ 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 @@ -11786,7 +11568,7 @@ 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 @@ -11899,6 +11681,9 @@ 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 @@ -11938,7 +11723,7 @@ 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 @@ -11987,7 +11772,7 @@ 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 @@ -12010,7 +11795,7 @@ 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 @@ -12125,7 +11910,7 @@ 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 @@ -12160,7 +11945,7 @@ 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 @@ -12201,7 +11986,7 @@ 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 @@ -12314,7 +12099,7 @@ 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 @@ -12347,7 +12132,7 @@ 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 @@ -12390,7 +12175,7 @@ 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 @@ -12596,7 +12381,7 @@ 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 @@ -12639,7 +12424,7 @@ 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."))) @@ -12676,7 +12461,7 @@ 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 @@ -12733,7 +12518,7 @@ 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."))) @@ -12770,7 +12555,7 @@ 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 @@ -12978,11 +12763,11 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rtracklayer" ,r-rtracklayer) ("r-rjson" ,r-rjson) ("salmon" ,salmon) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,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 @@ -12995,7 +12780,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.42") + (version "0.0.43") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -13003,7 +12788,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0xbvgqpk32a8iczhvac56cacr46rdkqb0allhhpvmj940idf72bi")))) + "0426i31b7mqqkbss5dgrvf5prkj4z1qrd7yrpd27vybs01xhdlks")))) (build-system gnu-build-system) ;; parts of the tests rely on access to the network (arguments '(#:tests? #f)) @@ -13040,8 +12825,8 @@ expression report comparing samples in an easily configurable manner.") ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) @@ -13051,7 +12836,7 @@ 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 @@ -13065,7 +12850,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.10") + (version "0.1.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -13073,10 +12858,13 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy")))) + "0mpzlay2d5cjpmrcp7knff6rg1c2mqszd638n7lw0mc0cycbp9f8")))) (build-system gnu-build-system) (arguments - `(#:phases + `(;; TODO: tests currently require 12+GB of RAM. See + ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164 + #:tests? #f + #:phases (modify-phases %standard-phases (add-before 'check 'set-timezone ;; The readr package is picky about timezones. @@ -13096,24 +12884,29 @@ in an easily configurable manner.") ("r-annotationhub" ,r-annotationhub) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) + ("r-ggrepel" ,r-ggrepel) ("r-methylkit" ,r-methylkit) ("r-rtracklayer" ,r-rtracklayer) ("r-rmarkdown" ,r-rmarkdown) ("r-bookdown" ,r-bookdown) ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("snakemake" ,snakemake) ("bismark" ,bismark) - ("fastqc" ,fastqc) ("bowtie" ,bowtie) + ("bwa-meth" ,bwa-meth) + ("fastqc" ,fastqc) + ("methyldackel" ,methyldackel) + ("multiqc" ,multiqc) ("trim-galore" ,trim-galore) ("cutadapt" ,cutadapt) + ("samblaster" ,samblaster) ("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 @@ -13147,8 +12940,8 @@ methylation and segmentation.") ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("pandoc" ,pandoc) + ("pandoc-citeproc" ,pandoc-citeproc) ("samtools" ,samtools) ("snakemake" ,snakemake) ("star" ,star) @@ -13177,7 +12970,7 @@ 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 @@ -13206,7 +12999,7 @@ 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: @@ -13230,7 +13023,7 @@ 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 @@ -13265,7 +13058,7 @@ 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 @@ -13291,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.") (supported-systems '("x86_64-linux")) (license license:bsd-3)))) -(define-public r-diversitree - (package - (name "r-diversitree") - (version "0.9-13") - (source - (origin - (method url-fetch) - (uri (cran-uri "diversitree" version)) - (sha256 - (base32 - "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-desolve" ,r-desolve) - ("r-rcpp" ,r-rcpp) - ("r-subplex" ,r-subplex))) - (home-page "https://www.zoology.ubc.ca/prog/diversitree") - (synopsis "Comparative 'phylogenetic' analyses of diversification") - (description "This package contains a number of comparative \"phylogenetic\" -methods, mostly focusing on analysing diversification and character evolution. -Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) -and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and -Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods -include Markov models of discrete and continuous trait evolution and constant -rate speciation and extinction.") - (license license:gpl2+))) - (define-public sjcount ;; There is no tag for version 3.2, nor is there a release archive. (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5") @@ -13332,7 +13094,7 @@ 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 @@ -13437,14 +13199,14 @@ 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))) @@ -13457,7 +13219,8 @@ 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 @@ -13476,7 +13239,7 @@ 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 @@ -13522,7 +13285,7 @@ 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 @@ -13556,7 +13319,7 @@ 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 @@ -13583,7 +13346,7 @@ 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 @@ -13863,7 +13626,7 @@ 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 @@ -13962,7 +13725,7 @@ 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 @@ -14002,7 +13765,7 @@ 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 @@ -14151,7 +13914,7 @@ 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 @@ -14184,7 +13947,7 @@ 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 @@ -14215,7 +13978,7 @@ 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 @@ -14263,7 +14026,7 @@ 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 @@ -14294,7 +14057,7 @@ 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 @@ -14320,33 +14083,6 @@ downstream analysis. Poretools operates directly on the native FAST5, a variant of the Hierarchical Data Format (HDF5) standard.") (license license:expat)))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public jamm (package (name "jamm") @@ -14355,7 +14091,7 @@ 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 @@ -14555,7 +14291,7 @@ 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 @@ -14616,7 +14352,7 @@ 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)) @@ -14690,7 +14426,7 @@ 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 @@ -14726,7 +14462,7 @@ 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 @@ -14989,7 +14725,7 @@ 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 @@ -15028,7 +14764,7 @@ 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 @@ -15250,7 +14986,7 @@ 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 @@ -15291,7 +15027,7 @@ 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 @@ -15322,7 +15058,7 @@ 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 @@ -15353,7 +15089,7 @@ 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 @@ -15414,12 +15150,34 @@ mutations from scRNA-Seq data.") (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") (string-append "INCLUDES= -I" htslib-ref "/include/htslib") "HTS_HEADERS=" ; No need to check for headers here. - (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (string-append "LIBPATH=-L. -L" htslib-ref "/include")) + (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts") + (invoke "ar" "rcs" "libtabixpp.a" "tabix.o")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "tabix++" bin)) - #t))))) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (install-file "tabix++" bin) + (install-file "libtabixpp.so" lib) + (install-file "libtabixpp.a" lib) + (install-file "tabix.hpp" (string-append out "/include")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + ~@ + Name: libtabixpp~@ + Version: ~a~@ + Description: C++ wrapper around tabix project~@ + Libs: -L${libdir} -ltabixpp~@ + Cflags: -I${includedir}~%" + out ,version))) + #t)))))) (home-page "https://github.com/ekg/tabixpp") (synopsis "C++ wrapper around tabix project") (description "This is a C++ wrapper around the Tabix project which abstracts @@ -15446,13 +15204,45 @@ some of the details of opening and jumping in tabix-indexed files.") #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #t)) + (add-after 'build 'build-dynamic + (lambda _ + (invoke "g++" + "-shared" "-o" "libsmithwaterman.so" + "smithwaterman.o" "SmithWatermanGotoh.o" + "disorder.o" "BandedSmithWaterman.o" + "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) (lib (string-append out "/lib"))) (install-file "smithwaterman" bin) - (install-file "libsw.a" lib)) + (for-each + (lambda (file) + (install-file file (string-append out "/include/smithwaterman"))) + (find-files "." "\\.h$")) + (install-file "libsmithwaterman.so" lib) + (install-file "libsw.a" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/smithwaterman~@ + ~@ + ~@ + Name: smithwaterman~@ + Version: ~a~@ + Description: smith-waterman-gotoh alignment algorithm~@ + Libs: -L${libdir} -lsmithwaterman~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") @@ -15542,10 +15332,43 @@ neural networks.") #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #t)) + (add-after 'build 'build-dynamic + (lambda _ + (invoke "g++" + "-shared" "-o" "libfastahack.so" + "Fasta.o" "FastaHack.o" "split.o" "disorder.o"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "fastahack" bin)) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (bin (string-append out "/bin"))) + (mkdir-p (string-append out "/include/fastahack")) + (for-each + (lambda (file) + (install-file file (string-append out "/include/fastahack"))) + (find-files "." "\\.h$")) + (install-file "fastahack" bin) + (install-file "libfastahack.so" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/fastahack~@ + ~@ + ~@ + Name: fastahack~@ + Version: ~a~@ + Description: Indexing and sequence extraction from FASTA files~@ + Libs: -L${libdir} -lfastahack~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/ekg/fastahack") (synopsis "Indexing and sequence extraction from FASTA files") @@ -15568,9 +15391,16 @@ library automatically handles index file generation and use.") "/vcflib-" version "-src.tar.gz")) (sha256 (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm")) + (patches (search-patches "vcflib-use-shared-libraries.patch")) (modules '((guix build utils))) (snippet `(begin + (substitute* (find-files "." "\\.(h|c)(pp)?$") + (("\"SmithWatermanGotoh.h\"") "") + (("\"convert.h\"") "") + (("\"disorder.h\"") "") + (("\"tabix.hpp\"") "") + (("\"Fasta.h\"") "")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" "libVCFH" "multichoose" "smithwaterman" "tabixpp")) @@ -15578,34 +15408,34 @@ library automatically handles index file generation and use.") (build-system gnu-build-system) (inputs `(("htslib" ,htslib) + ("fastahack" ,fastahack) ("perl" ,perl) ("python" ,python) + ("smithwaterman" ,smithwaterman) + ("tabixpp" ,tabixpp) + ("xz" ,xz) ("zlib" ,zlib))) (native-inputs - `(;; Submodules. + `(("pkg-config" ,pkg-config) + ;; Submodules. ;; This package builds against the .o files so we need to extract the source. - ("fastahack-src" ,(package-source fastahack)) ("filevercmp-src" ,(package-source filevercmp)) - ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) - ("multichoose-src" ,(package-source multichoose)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("tabixpp-src" ,(package-source tabixpp)))) + ("multichoose-src" ,(package-source multichoose)))) (arguments `(#:tests? #f ; no tests - #:make-flags (list (string-append "HTS_LIB=" - (assoc-ref %build-inputs "htslib") - "/lib/libhts.a") - (string-append "HTS_INCLUDES= -I" - (assoc-ref %build-inputs "htslib") - "/include/htslib") - (string-append "HTS_LDFLAGS= -L" - (assoc-ref %build-inputs "htslib") - "/include/htslib" " -lhts")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'set-flags + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("LDFLAGS =") + (string-append "LDFLAGS = -Wl,-rpath=" + (assoc-ref outputs "out") "/lib "))) + (substitute* "filevercmp/Makefile" + (("-c") "-c -fPIC")) + #t)) (delete 'configure) - (delete 'check) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -15617,34 +15447,39 @@ library automatically handles index file generation and use.") (assoc-ref inputs source) "--strip-components=1")))))) (and - (unpack "fastahack-src" "fastahack") (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (let ((htslib (assoc-ref inputs "htslib"))) - (with-directory-excursion "tabixpp" - (substitute* "Makefile" - (("-Ihtslib") (string-append "-I" htslib "/include/htslib")) - (("-Lhtslib") (string-append "-L" htslib "/lib/htslib")) - (("htslib/htslib") (string-append htslib "/include/htslib"))) - (invoke "make" - (string-append "HTS_LIB=" htslib "/lib/libhts.a"))) - (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags)))) + (unpack "multichoose-src" "multichoose"))))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) (for-each (lambda (file) (install-file file bin)) (find-files "bin" ".*")) - ;; The header files in src/ do not interface libvcflib, - ;; therefore they are left out. - (install-file "libvcflib.a" lib)) + (install-file "libvcflib.so" lib) + (install-file "libvcflib.a" lib) + (for-each + (lambda (file) + (install-file file (string-append out "/include"))) + (find-files "include" "\\.h(pp)?$")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + ~@ + Name: libvcflib~@ + Version: ~a~@ + Requires: smithwaterman, fastahack~@ + Description: C++ library for parsing and manipulating VCF files~@ + Libs: -L${libdir} -lvcflib~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") @@ -15665,7 +15500,7 @@ 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 @@ -15783,7 +15618,7 @@ 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 @@ -15820,7 +15655,7 @@ 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 @@ -15861,7 +15696,7 @@ 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 @@ -15898,6 +15733,77 @@ containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) +;; This package bundles PCRE 8.02 and cannot be built with the current +;; version. +(define-public phast + (package + (name "phast") + (version "1.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/CshlSiepelLab/phast") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list "CC=gcc" + (string-append "DESTDIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Fix syntax + (substitute* "test/Makefile" + ((" ") " ")) + (substitute* "Makefile" + (("CLAPACKPATH=/usr/lib") + (string-append "CLAPACKPATH=" + (assoc-ref inputs "clapack") "/lib"))) + ;; Renaming the libraries is not necessary with our version of + ;; CLAPACK. + (substitute* "src/lib/Makefile" + (("ifdef CLAPACKPATH") "ifdef UNNECESSARY")) + (substitute* "src/make-include.mk" + (("-lblaswr") "-lblas") + (("-ltmg") "-ltmglib") + (("liblapack.a") "liblapack.so") + (("libblas.a") "libblas.so") + (("libf2c.a") "libf2c.so")) + (substitute* "src/Makefile" + (("/opt") "/share") + (("/usr/") "/")) + #t)) + (replace 'check + (lambda _ + (setenv "PATH" + (string-append (getcwd) "/bin:" (getenv "PATH"))) + ;; Disable broken test + (substitute* "test/Makefile" + ((".*if.*hmrc_summary" m) (string-append "#" m))) + ;; Only run the msa_view tests because the others fail for + ;; unknown reasons. + (invoke "make" "-C" "test" "msa_view")))))) + (inputs + `(("clapack" ,clapack))) + (native-inputs + `(("perl" ,perl))) + (home-page "http://compgen.cshl.edu/phast/") + (synopsis "Phylogenetic analysis with space/time models") + (description + "Phylogenetic Analysis with Space/Time models (PHAST) is a collection of +command-line programs and supporting libraries for comparative and +evolutionary genomics. Best known as the search engine behind the +Conservation tracks in the University of California, Santa Cruz (UCSC) Genome +Browser, PHAST also includes several tools for phylogenetic modeling, +functional element identification, as well as utilities for manipulating +alignments, trees and genomic annotations.") + (license license:bsd-3))) + (define-public python-gffutils ;; The latest release is older more than a year than the latest commit (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") @@ -15909,7 +15815,7 @@ 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