X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/c61268c1b74557bf6b8a26a9c95a47b1bea39d20..3832704aff7444e26ba7f6915bdb4f718b1bf2f4:/gnu/packages/bioinformatics.scm diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8bd42c9429..5efcfdea11 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft -;;; Copyright © 2015, 2016 Pjotr Prins +;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2020 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner @@ -11,13 +11,14 @@ ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu -;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2020 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 Pierre Langlois +;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; ;;; This file is part of GNU Guix. ;;; @@ -65,6 +66,8 @@ #: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) @@ -81,6 +84,7 @@ #: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) @@ -90,6 +94,7 @@ #: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) @@ -102,6 +107,7 @@ #: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) @@ -112,10 +118,12 @@ #: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) @@ -313,7 +321,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" @@ -321,11 +329,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.11") #t)))) (build-system gnu-build-system) (arguments @@ -354,6 +362,28 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) +(define-public bcftools-1.9 + (package (inherit bcftools) + (name "bcftools") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/samtools/bcftools/" + "releases/download/" + version "/bcftools-" version ".tar.bz2")) + (sha256 + (base32 + "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (build-system gnu-build-system) + (native-inputs + `(("htslib" ,htslib-1.9) + ("perl" ,perl))))) + (define-public bedops (package (name "bedops") @@ -437,7 +467,7 @@ computational cluster.") (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) + `(("samtools" ,samtools-1.9) ("zlib" ,zlib))) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") @@ -1955,7 +1985,7 @@ multiple sequence alignments.") ;; FIXME: tests keep timing out on some systems. (invoke "nosetests" "-v" "--processes" "1"))))))) (propagated-inputs - `(("htslib" ,htslib))) ; Included from installed header files. + `(("htslib" ,htslib-1.9))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("curl" ,curl) @@ -1963,8 +1993,8 @@ multiple sequence alignments.") (native-inputs `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. - ("samtools" ,samtools) - ("bcftools" ,bcftools) + ("samtools" ,samtools-1.9) + ("bcftools" ,bcftools-1.9) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") @@ -2557,6 +2587,132 @@ accessing bigWig files.") (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") @@ -4009,6 +4165,7 @@ VCF.") ;; [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") @@ -4086,7 +4243,7 @@ VCF.") `(("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) @@ -4215,7 +4372,7 @@ performance.") (define-public htslib (package (name "htslib") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) (uri (string-append @@ -4223,8 +4380,15 @@ performance.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) + "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng")))) (build-system gnu-build-system) + ;; Let htslib translate "gs://" and "s3://" to regular https links with + ;; "--enable-gcs" and "--enable-s3". For these options to work, we also + ;; need to set "--enable-libcurl". + (arguments + `(#:configure-flags '("--enable-gcs" + "--enable-libcurl" + "--enable-s3"))) (inputs `(("curl" ,curl) ("openssl" ,openssl))) @@ -4243,6 +4407,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public htslib-1.9 + (package (inherit htslib) + (name "htslib") + (version "1.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/samtools/htslib/releases/download/" + version "/htslib-" version ".tar.bz2")) + (sha256 + (base32 + "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))))) + ;; This package should be removed once no packages rely upon it. (define htslib-1.3 (package @@ -4463,26 +4640,40 @@ experiments.") ;; The PyPi tarball does not contain tests. (method git-fetch) (uri (git-reference - (url "https://github.com/taoliu/MACS") + (url "https://github.com/macs3-project/MACS") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15")))) + "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15")) + (modules '((guix build utils))) + ;; Remove files generated by Cython + (snippet + '(begin + (for-each (lambda (file) + (let ((generated-file + (string-append (string-drop-right file 3) "c"))) + (when (file-exists? generated-file) + (delete-file generated-file)))) + (find-files "." "\\.pyx$")) + (delete-file "MACS2/IO/CallPeakUnitPrecompiled.c") + #t)))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v")))))) + (replace 'check + (lambda* (#:key tests? inputs outputs #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-v")) + #t))))) (inputs `(("python-numpy" ,python-numpy))) (native-inputs - `(("python-pytest" ,python-pytest))) - (home-page "https://github.com/taoliu/MACS/") + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest))) + (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description "MACS is an implementation of a ChIP-Seq analysis algorithm for @@ -4496,7 +4687,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.394") + (version "7.471") (source (origin (method url-fetch) (uri (string-append @@ -4505,7 +4696,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b")))) + "0r1973fx2scq4712zdqfy67wkzqj0c0bhrdy4jxhvq40mdxyry30")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -4568,7 +4759,7 @@ sequencing tag position and orientation.") ("gawk" ,gawk) ("grep" ,grep) ("coreutils" ,coreutils))) - (home-page "http://mafft.cbrc.jp/alignment/software/") + (home-page "https://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description "MAFFT offers a range of multiple alignment methods for nucleotide and @@ -4576,7 +4767,7 @@ protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).") (license (license:non-copyleft - "http://mafft.cbrc.jp/alignment/software/license.txt" + "https://mafft.cbrc.jp/alignment/software/license.txt" "BSD-3 with different formatting")))) (define-public mash @@ -5606,7 +5797,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.9") + (version "1.11") (source (origin (method url-fetch) @@ -5615,11 +5806,11 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.11") #t)))) (build-system gnu-build-system) (arguments @@ -5665,6 +5856,31 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) +(define-public samtools-1.9 + (package (inherit samtools) + (name "samtools") + (version "1.9") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/samtools/samtools/" + version "/samtools-" version ".tar.bz2")) + (sha256 + (base32 + "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + (modules '((guix build utils))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.9") + #t)))) + (inputs + `(("htslib" ,htslib-1.9) + ("ncurses" ,ncurses) + ("perl" ,perl) + ("python" ,python) + ("zlib" ,zlib))))) + (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input ;; and output formats differ greatly from that used and produced by samtools @@ -7539,13 +7755,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "07rjl2n4sazdg581zh7w3yykzphgr2gpz41ba4ryqs7347vh9nbf")))) + "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -8848,13 +9064,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.2") + (version "2.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j")))) + "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -10272,14 +10488,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.20.0") + (version "1.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j")))) + "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10599,91 +10815,6 @@ EMBL-EBI GWAS catalog.") visualizations for publication-quality multi-panel figures.") (license license:gpl2+))) -(define-public r-fithic - (package - (name "r-fithic") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "FitHiC" version)) - (sha256 - (base32 - "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) - (properties `((upstream-name . "FitHiC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/FitHiC") - (synopsis "Confidence estimation for intra-chromosomal contact maps") - (description - "Fit-Hi-C is a tool for assigning statistical confidence estimates to -intra-chromosomal contact maps produced by genome-wide genome architecture -assays such as Hi-C.") - (license license:gpl2+))) - -(define-public r-hitc - (package - (name "r-hitc") - (version "1.32.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HiTC" version)) - (sha256 - (base32 - "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) - (properties `((upstream-name . "HiTC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) - (home-page "https://bioconductor.org/packages/HiTC") - (synopsis "High throughput chromosome conformation capture analysis") - (description - "The HiTC package was developed to explore high-throughput \"C\" data -such as 5C or Hi-C. Dedicated R classes as well as standard methods for -quality controls, normalization, visualization, and further analysis are also -provided.") - (license license:artistic2.0))) - -(define-public r-hdf5array - (package - (name "r-hdf5array") - (version "1.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "HDF5Array" version)) - (sha256 - (base32 - "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) - (properties `((upstream-name . "HDF5Array"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/HDF5Array") - (synopsis "HDF5 back end for DelayedArray objects") - (description "This package provides an array-like container for convenient -access and manipulation of HDF5 datasets. It supports delayed operations and -block processing.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -11032,7 +11163,7 @@ programs for inferring phylogenies (evolutionary trees).") (define-public imp (package (name "imp") - (version "2.6.2") + (version "2.13.0") (source (origin (method url-fetch) @@ -11040,25 +11171,47 @@ programs for inferring phylogenies (evolutionary trees).") version "/download/imp-" version ".tar.gz")) (sha256 (base32 - "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) + "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) - ("python" ,python-2))) + ("eigen" ,eigen) + ;; 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 @@ -11076,7 +11229,7 @@ applications for tackling some common problems in a user-friendly way.") (define-public tadbit (package (name "tadbit") - (version "0.2.0") + (version "1.0.1") (source (origin (method git-fetch) (uri (git-reference @@ -11085,21 +11238,13 @@ applications for tackling some common problems in a user-friendly way.") (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" @@ -11111,15 +11256,25 @@ applications for tackling some common problems in a user-friendly way.") "/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 @@ -11232,7 +11387,6 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) - ("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("openssl" ,openssl-1.0))) (home-page "https://genome.cse.ucsc.edu/index.html") @@ -12528,7 +12682,7 @@ expression report comparing samples in an easily configurable manner.") (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/" @@ -12536,7 +12690,7 @@ expression report comparing samples in an easily configurable manner.") "/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)) @@ -12548,23 +12702,30 @@ expression report comparing samples in an easily configurable manner.") ("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) @@ -12665,7 +12826,7 @@ methylation and segmentation.") (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/" @@ -12673,7 +12834,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9")))) + "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) @@ -12895,21 +13056,26 @@ version does count multisplits.") "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) @@ -15440,7 +15606,7 @@ patterns.") (define-public methyldackel (package (name "methyldackel") - (version "0.4.0") + (version "0.5.1") (source (origin (method git-fetch) (uri (git-reference @@ -15449,7 +15615,7 @@ patterns.") (file-name (git-file-name name version)) (sha256 (base32 - "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + "1sfhf2ap75qxpnmy1ifgmxqs18rq8mah9mcgkby73vc6h0sw99ws")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -15462,11 +15628,14 @@ patterns.") (replace 'configure (lambda* (#:key outputs #:allow-other-keys) (substitute* "Makefile" + (("-lhts ") "-lhts -lBigWig ") (("install MethylDackel \\$\\(prefix\\)" match) (string-append "install -d $(prefix); " match))) #t))))) (inputs - `(("htslib" ,htslib) + `(("curl" ,curl) ; XXX: needed by libbigwig + ("htslib" ,htslib-1.9) + ("libbigwig" ,libbigwig) ("zlib" ,zlib))) ;; Needed for tests (native-inputs @@ -15629,7 +15798,7 @@ than is possible with plain-text methods alone.") (propagated-inputs `(("libxml2" ,libxml2))) (native-inputs - `(("check" ,check) + `(("check" ,check-0.14) ("swig" ,swig))) (home-page "http://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams")