;;; 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 © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
-;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; 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 bcftools
(package
(name "bcftools")
- (version "1.9")
+ (version "1.11")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
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
;; 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")
(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")
;; 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)
(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")
(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 htslib
(package
(name "htslib")
- (version "1.9")
+ (version "1.11")
(source (origin
(method url-fetch)
(uri (string-append
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)))
;; 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
;; 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
(define-public mafft
(package
(name "mafft")
- (version "7.394")
+ (version "7.471")
(source (origin
(method url-fetch)
(uri (string-append
(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
("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
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
(define-public samtools
(package
(name "samtools")
- (version "1.9")
+ (version "1.11")
(source
(origin
(method url-fetch)
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
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
(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)
(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)))
(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
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"))
(define-public imp
(package
(name "imp")
- (version "2.6.2")
+ (version "2.13.0")
(source
(origin
(method url-fetch)
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
(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
("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")
(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)
(define-public methyldackel
(package
(name "methyldackel")
- (version "0.4.0")
+ (version "0.5.1")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g"))))
+ "1sfhf2ap75qxpnmy1ifgmxqs18rq8mah9mcgkby73vc6h0sw99ws"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
(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
(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")
HCoop / jackhill / guix / guix.git / blobdiff