;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2015, 2016
, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
-;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages code)
+ #:use-module (gnu packages commencement)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages cran)
#:use-module (gnu packages golang)
#:use-module (gnu packages glib)
#:use-module (gnu packages graph)
+ #:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages groff)
#:use-module (gnu packages gtk)
#:use-module (gnu packages haskell-web)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
+ #:use-module (gnu packages image-processing)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages java-compression)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages node)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages parallel)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
(define-public python2-pybigwig
(package-with-python2 python-pybigwig))
+(define-public python-schema-salad
+ (package
+ (name "python-schema-salad")
+ (version "7.0.20200811075006")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol-0.11)
+ ("python-lockfile" ,python-lockfile)
+ ("python-mistune" ,python-mistune)
+ ("python-rdflib" ,python-rdflib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-requests" ,python-requests)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-typing-extensions" ,python-typing-extensions)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://github.com/common-workflow-language/schema_salad")
+ (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
+ (description
+ "Salad is a schema language for describing JSON or YAML structured linked
+data documents. Salad schema describes rules for preprocessing, structural
+validation, and hyperlink checking for documents described by a Salad schema.
+Salad supports rich data modeling with inheritance, template specialization,
+object identifiers, object references, documentation generation, code
+generation, and transformation to RDF. Salad provides a bridge between document
+and record oriented data modeling and the Semantic Web.")
+ (license license:asl2.0)))
+
+(define-public cwltool
+ (package
+ (name "cwltool")
+ (version "3.0.20201121085451")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/common-workflow-language/cwltool")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-restrictions
+ (lambda _
+ (substitute* "setup.py"
+ (("== 1.5.1") ">=1.5.1") ; prov
+ ((", < 3.5") "")) ; shellescape
+ #t))
+ (add-after 'unpack 'dont-use-git
+ (lambda _
+ (substitute* "gittaggers.py"
+ (("self.git_timestamp_tag\\(\\)")
+ (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
+ (string-drop ,version 4) ")))")))
+ #t))
+ (add-after 'unpack 'modify-tests
+ (lambda _
+ ;; Tries to connect to the internet.
+ (delete-file "tests/test_udocker.py")
+ (delete-file "tests/test_http_input.py")
+ (substitute* "tests/test_load_tool.py"
+ (("def test_load_graph_fragment_from_packed")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_load_graph_fragment_from_packed")))
+ (substitute* "tests/test_examples.py"
+ (("def test_env_filtering")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_env_filtering")))
+ ;; Tries to use cwl-runners.
+ (substitute* "tests/test_examples.py"
+ (("def test_v1_0_arg_empty_prefix_separate_false")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_v1_0_arg_empty_prefix_separate_false")))
+ #t)))))
+ (propagated-inputs
+ `(("python-argcomplete" ,python-argcomplete)
+ ("python-bagit" ,python-bagit)
+ ("python-coloredlogs" ,python-coloredlogs)
+ ("python-mypy-extensions" ,python-mypy-extensions)
+ ("python-prov" ,python-prov)
+ ("python-pydot" ,python-pydot)
+ ("python-psutil" ,python-psutil)
+ ("python-rdflib" ,python-rdflib)
+ ("python-requests" ,python-requests)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-schema-salad" ,python-schema-salad)
+ ("python-shellescape" ,python-shellescape)
+ ("python-typing-extensions" ,python-typing-extensions)
+ ;; Not listed as needed but still necessary:
+ ("node" ,node)))
+ (native-inputs
+ `(("python-arcp" ,python-arcp)
+ ("python-humanfriendly" ,python-humanfriendly)
+ ("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-mock" ,python-pytest-mock)
+ ("python-pytest-runner" ,python-pytest-runner)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)))
+ (home-page
+ "https://github.com/common-workflow-language/common-workflow-language")
+ (synopsis "Common Workflow Language reference implementation")
+ (description
+ "This is the reference implementation of the @acronym{CWL, Common Workflow
+Language} standards. The CWL open standards are for describing analysis
+workflows and tools in a way that makes them portable and scalable across a
+variety of software and hardware environments, from workstations to cluster,
+cloud, and high performance computing (HPC) environments. CWL is designed to
+meet the needs of data-intensive science, such as Bioinformatics, Medical
+Imaging, Astronomy, Physics, and Chemistry. The @acronym{cwltool, CWL reference
+implementation} is intended to be feature complete and to provide comprehensive
+validation of CWL files as well as provide other tools related to working with
+CWL descriptions.")
+ (license license:asl2.0)))
+
(define-public python-dendropy
(package
(name "python-dendropy")
;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
#:tests? #f
#:jdk ,icedtea-8
+ #:ant ,ant/java8
;; This is only used for tests.
#:make-flags
(list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
`(("java-snappy-1" ,java-snappy-1)
("java-commons-jexl-2" ,java-commons-jexl-2)
("java-cofoja" ,java-cofoja)
- ("ant" ,ant) ; for bzip2 support at runtime
+ ("ant" ,ant/java8) ; for bzip2 support at runtime
("zlib" ,zlib)))
(native-inputs
`(("ant-apache-bcel" ,ant-apache-bcel)
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g"))))
+ "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp"))))
+ "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.34.1")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl"))))
+ "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.30.1")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw"))))
+ "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy"))))
+ "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.50.1")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j"))))
+ "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-category
(package
(name "r-category")
- (version "2.54.0")
+ (version "2.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b"))))
+ "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.54.0")
+ (version "2.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9"))))
+ "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d"))))
+ "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
+ ("r-rhtslib" ,r-rhtslib)
("r-hwriter" ,r-hwriter)
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.22.0")
+ (version "1.24.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2"))))
+ "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
("r-ggplot2" ,r-ggplot2)
("r-go-db" ,r-go-db)
("r-gostats" ,r-gostats)
+ ("r-iranges" ,r-iranges)
("r-limma" ,r-limma)
("r-magrittr" ,r-magrittr)
("r-pheatmap" ,r-pheatmap)
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb"))))
+ "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.56.2")
+ (version "1.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w"))))
+ "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.16.1")
+ (version "2.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7"))))
+ "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny"))))
+ "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.26.1")
+ (version "0.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb"))))
+ "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.22.2")
+ (version "2.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d"))))
+ "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.24.2")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd"))))
+ "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.30.3")
+ (version "3.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic"))))
+ "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw"))))
+ "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-matrixgenerics" ,r-matrixgenerics)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
(define-public r-limma
(package
(name "r-limma")
- (version "3.44.3")
+ (version "3.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6"))))
+ "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.28.0")
+ (version "0.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc"))))
+ "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.40.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1"))))
+ "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.48.0")
+ (version "2.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp"))))
+ "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.50.3")
+ (version "1.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3"))))
+ "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.44.1")
+ (version "2.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz"))))
+ "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
("r-progress" ,r-progress)
("r-rappdirs" ,r-rappdirs)
("r-stringr" ,r-stringr)
- ("r-xml" ,r-xml)))
+ ("r-xml" ,r-xml)
+ ("r-xml2" ,r-xml2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/biomaRt")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.22.0")
+ (version "1.24.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g"))))
+ "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.56.0")
+ (version "2.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8"))))
+ "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "2.4.0")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq"))))
+ "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.14.1")
+ (version "0.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v"))))
+ "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)))
+ ("r-matrixgenerics" ,r-matrixgenerics)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/DelayedArray")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.18.2")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw"))))
+ "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
+ ("r-matrixgenerics" ,r-matrixgenerics)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d"))))
+ "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.48.0")
+ (version "1.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf"))))
+ "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
(build-system r-build-system)
(arguments
`(#:phases
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)))
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
(home-page "https://bioconductor.org/packages/rtracklayer")
(synopsis "R interface to genome browsers and their annotation tracks")
(description
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.40.1")
+ (version "1.42.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z"))))
+ "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.40.0")
+ (version "2.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr"))))
+ "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.56.0")
+ (version "1.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6"))))
+ "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
(define-public r-impute
(package
(name "r-impute")
- (version "1.62.0")
+ (version "1.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h"))))
+ "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
(native-inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.14.2")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l"))))
+ "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
"1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
(build-system cmake-build-system)
(arguments
- `(;; FIXME: Some tests fail because they produce warnings, others fail
- ;; because the PYTHONPATH does not include the modeller's directory.
- #:tests? #f))
+ `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used
+ ;; below to have an effect.
+ #:cmake ,cmake
+ #:configure-flags
+ (let ((disabled-tests
+ '("expensive" ;exclude expensive tests
+ "IMP.modeller" ;fail to import its own modules
+ "IMP.parallel-test_sge.py" ;fail in build container
+ ;; The following test fails non-reproducibly on
+ ;; an inexact numbers assertion.
+ "IMP.em-medium_test_local_fitting.py")))
+ (list
+ (string-append
+ "-DCMAKE_CTEST_ARGUMENTS="
+ (string-join
+ (list "-L" "-tests?-" ;select only tests
+ "-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
+ ";"))))))
+ (native-inputs
+ `(("python" ,python-wrapper)
+ ("swig" ,swig)))
(inputs
`(("boost" ,boost)
+ ("cgal" ,cgal)
("gsl" ,gsl)
- ("swig" ,swig)
("hdf5" ,hdf5)
("fftw" ,fftw)
("eigen" ,eigen)
- ("python" ,python-2)))
+ ;; Enabling MPI causes the build to use all the available memory and
+ ;; fail (tested on a machine with 32 GiB of RAM).
+ ;;("mpi" ,openmpi)
+ ("opencv" ,opencv)))
(propagated-inputs
- `(("python2-numpy" ,python2-numpy)
- ("python2-scipy" ,python2-scipy)
- ("python2-pandas" ,python2-pandas)
- ("python2-scikit-learn" ,python2-scikit-learn)
- ("python2-networkx" ,python2-networkx)))
+ `(("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)
+ ("python-pandas" ,python-pandas)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-networkx" ,python-networkx)))
(home-page "https://integrativemodeling.org")
(synopsis "Integrative modeling platform")
(description "IMP's broad goal is to contribute to a comprehensive
(define-public tadbit
(package
(name "tadbit")
- (version "0.2.0")
+ (version "1.0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
+ "0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni"))))
(build-system python-build-system)
(arguments
- `(;; Tests are included and must be run after installation, but
- ;; they are incomplete and thus cannot be run.
- #:tests? #f
- #:python ,python-2
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-problems-with-setup.py
(lambda* (#:key outputs #:allow-other-keys)
- ;; setup.py opens these files for writing
- (chmod "_pytadbit/_version.py" #o664)
- (chmod "README.rst" #o664)
-
;; Don't attempt to install the bash completions to
;; the home directory.
(rename-file "extras/.bash_completion"
"/etc/bash_completion.d\""))
(("extras/\\.bash_completion")
"extras/tadbit"))
+ #t))
+ (replace 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python3" "test/test_all.py")
#t)))))
+ (native-inputs
+ `(("glib" ,glib "bin") ;for gtester
+ ("pkg-config" ,pkg-config)))
(inputs
;; TODO: add Chimera for visualization
`(("imp" ,imp)
("mcl" ,mcl)
- ("python2-scipy" ,python2-scipy)
- ("python2-numpy" ,python2-numpy)
- ("python2-matplotlib" ,python2-matplotlib)
- ("python2-pysam" ,python2-pysam)))
+ ("python-future" ,python-future)
+ ("python-h5py" ,python-h5py)
+ ("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pysam" ,python-pysam)))
(home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data")
(description
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.43")
+ (version "0.0.51")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "0426i31b7mqqkbss5dgrvf5prkj4z1qrd7yrpd27vybs01xhdlks"))))
+ "0bb6hzpl0qq0jd57pgd1m5ns547rfipr6071a4m12vxlm4nlpi5q"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))
("r-biocparallel" ,r-biocparallel)
("r-biostrings" ,r-biostrings)
("r-chipseq" ,r-chipseq)
+ ("r-corrplot" ,r-corrplot)
("r-data-table" ,r-data-table)
+ ("r-deseq2" ,r-deseq2)
("r-dplyr" ,r-dplyr)
+ ("r-dt" ,r-dt)
("r-genomation" ,r-genomation)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-gprofiler2" ,r-gprofiler2)
+ ("r-heatmaply" ,r-heatmaply)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plotly" ,r-plotly)
+ ("r-rmarkdown" ,r-rmarkdown)
("r-rsamtools" ,r-rsamtools)
+ ("r-rsubread" ,r-rsubread)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
- ("r-jsonlite" ,r-jsonlite)
- ("r-heatmaply" ,r-heatmaply)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-ggplot2" ,r-ggplot2)
- ("r-plotly" ,r-plotly)
- ("r-rmarkdown" ,r-rmarkdown)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
("python-magic" ,python-magic)
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "1.1.4")
+ (version "1.1.7")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9"))))
+ "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
(build-system gnu-build-system)
(inputs
`(("coreutils" ,coreutils)
"minimap2-" version ".tar.bz2"))
(sha256
(base32
- "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
+ "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))
+ (patches (search-patches "minimap2-aarch64-support.patch"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
#:make-flags
- (list "CC=gcc"
+ (list (string-append "CC=" ,(cc-for-target))
(let ((system ,(or (%current-target-system)
(%current-system))))
(cond
- ((string-prefix? "x86_64" system)
- "all")
- ((or (string-prefix? "armhf" system)
- (string-prefix? "aarch64" system))
- "arm_neon=1")
- (else "sse2only=1"))))
+ ((string-prefix? "x86_64" system)
+ "all")
+ ((or (string-prefix? "i586" system)
+ (string-prefix? "i686" system))
+ "sse2only=1")
+ ((string-prefix? "armhf" system)
+ "arm_neon=1")
+ ((string-prefix? "aarch64" system)
+ "aarch64=1")
+ (else ""))))
#:phases
(modify-phases %standard-phases
(delete 'configure)
HCoop / jackhill / guix / guix.git / blobdiff