diff options
author | Efraim Flashner <efraim@flashner.co.il> | 2021-04-16 14:39:48 +0300 |
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committer | Efraim Flashner <efraim@flashner.co.il> | 2021-04-16 14:39:48 +0300 |
commit | fcc39864dba82e14895afbe841091091366c96bc (patch) | |
tree | 6e0f05495fd6512051224dc85fd3ab495cbf1a24 /gnu/packages/bioinformatics.scm | |
parent | 76fc36d0a7215979bb74c05840f5a4de4ab5ea93 (diff) | |
parent | 44f9432705d04c069a8acf9e37e3ad856ac0bf82 (diff) |
Merge remote-tracking branch 'origin/master' into core-updates
Conflicts:
gnu/local.mk
gnu/packages/boost.scm
gnu/packages/chez.scm
gnu/packages/compression.scm
gnu/packages/crates-io.scm
gnu/packages/docbook.scm
gnu/packages/engineering.scm
gnu/packages/gcc.scm
gnu/packages/gl.scm
gnu/packages/gtk.scm
gnu/packages/nettle.scm
gnu/packages/python-check.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/rust.scm
gnu/packages/sqlite.scm
guix/build-system/node.scm
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 368 |
1 files changed, 37 insertions, 331 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e008ca16fb..313c70784a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2017, 2021 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> @@ -2546,15 +2546,27 @@ accessing bigWig files.") (define-public python-schema-salad (package (name "python-schema-salad") - (version "7.0.20200811075006") + (version "7.1.20210316164414") (source (origin (method url-fetch) (uri (pypi-uri "schema-salad" version)) (sha256 (base32 - "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg")))) + "04jaykdpgfnkrghvli5swxzqp7yba842am4bz42hcfljsmkrxvrk")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'skip-failing-tests + (lambda _ + ;; Skip tests that require network access. + (substitute* "schema_salad/tests/test_cwl11.py" + (("^def test_(secondaryFiles|outputBinding)" all) + (string-append "@pytest.mark.skip(reason=" + "\"test requires network access\")\n" + all))) + #t))))) (propagated-inputs `(("python-cachecontrol" ,python-cachecontrol-0.11) ("python-lockfile" ,python-lockfile) @@ -2582,7 +2594,7 @@ and record oriented data modeling and the Semantic Web.") (define-public cwltool (package (name "cwltool") - (version "3.0.20201121085451") + (version "3.0.20210319143721") (source (origin (method git-fetch) (uri (git-reference @@ -2591,7 +2603,7 @@ and record oriented data modeling and the Semantic Web.") (file-name (git-file-name name version)) (sha256 (base32 - "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w")))) + "1sgs9ckyxb9f9169mc3wm9lnjg4080ai42xqsrwpw9l8apy4c9m5")))) (build-system python-build-system) (arguments `(#:phases @@ -2599,8 +2611,9 @@ and record oriented data modeling and the Semantic Web.") (add-after 'unpack 'loosen-version-restrictions (lambda _ (substitute* "setup.py" - (("== 1.5.1") ">=1.5.1") ; prov - ((", < 3.5") "")) ; shellescape + (("== 1.5.1") ">=1.5.1") ; prov + ((", < 3.5") "") ; shellescape + ((" >= 6.0.2, < 6.2") "")) ; pytest #t)) (add-after 'unpack 'dont-use-git (lambda _ @@ -2612,6 +2625,7 @@ and record oriented data modeling and the Semantic Web.") (add-after 'unpack 'modify-tests (lambda _ ;; Tries to connect to the internet. + (delete-file "tests/test_content_type.py") (delete-file "tests/test_udocker.py") (delete-file "tests/test_http_input.py") (substitute* "tests/test_load_tool.py" @@ -6235,7 +6249,7 @@ subsequent visualization, annotation and storage of results.") (define-public plink-ng (package (inherit plink) (name "plink-ng") - (version "1.90b4") + (version "2.00a2.3") (source (origin (method git-fetch) @@ -6244,29 +6258,26 @@ subsequent visualization, annotation and storage of results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0")))) + (base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd")))) (build-system gnu-build-system) (arguments - '(#:tests? #f ;no "check" target + `(#:tests? #f ;no "check" target #:make-flags (list "BLASFLAGS=-llapack -lopenblas" "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" "ZLIB=-lz" - "-f" "Makefile.std") + "BIN=plink prettify" + (string-append "CC=" ,(cc-for-target)) + (string-append "PREFIX=" (assoc-ref %outputs "out")) + "DESTDIR=") #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ (chdir "1.9") #t)) - (delete 'configure) ; no "configure" script - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin/"))) - (install-file "plink" bin) - #t)))))) + (delete 'configure)))) ; no "configure" script (inputs - `(("zlib" ,zlib) - ("lapack" ,lapack) - ("openblas" ,openblas))) + `(("lapack" ,lapack) + ("openblas" ,openblas) + ("zlib" ,zlib))) (home-page "https://www.cog-genomics.org/plink/") (license license:gpl3+))) @@ -6728,9 +6739,9 @@ of these reads to align data quickly through a hash-based indexing scheme.") (synopsis "Biological sequence analysis tool for NGS reads") (description "SortMeRNA is a biological sequence analysis tool for filtering, mapping -and operational taxonomic unit (OTU) picking of next generation -sequencing (NGS) reads. The core algorithm is based on approximate seeds and -allows for fast and sensitive analyses of nucleotide sequences. The main +and @acronym{OTU, operational taxonomic unit} picking of @acronym{NGS, next +generation sequencing} reads. The core algorithm is based on approximate seeds +and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.") ;; The source includes x86 specific code (supported-systems '("x86_64-linux" "i686-linux")) @@ -7622,311 +7633,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-limma - (package - (name "r-limma") - (version "3.46.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "limma" version)) - (sha256 - (base32 - "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") - (description "This package can be used for the analysis of gene expression -studies, especially the use of linear models for analysing designed experiments -and the assessment of differential expression. The analysis methods apply to -different technologies, including microarrays, RNA-seq, and quantitative PCR.") - (license license:gpl2+))) - -(define-public r-xvector - (package - (name "r-xvector") - (version "0.30.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "XVector" version)) - (sha256 - (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) - (properties - `((upstream-name . "XVector"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/XVector") - (synopsis "Representation and manpulation of external sequences") - (description - "This package provides memory efficient S4 classes for storing sequences -\"externally\" (behind an R external pointer, or on disk).") - (license license:artistic2.0))) - -(define-public r-genomicranges - (package - (name "r-genomicranges") - (version "1.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicRanges" version)) - (sha256 - (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) - (properties - `((upstream-name . "GenomicRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicRanges") - (synopsis "Representation and manipulation of genomic intervals") - (description - "This package provides tools to efficiently represent and manipulate -genomic annotations and alignments is playing a central role when it comes to -analyzing high-throughput sequencing data (a.k.a. NGS data). The -GenomicRanges package defines general purpose containers for storing and -manipulating genomic intervals and variables defined along a genome.") - (license license:artistic2.0))) - -(define-public r-biobase - (package - (name "r-biobase") - (version "2.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biobase" version)) - (sha256 - (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) - (properties - `((upstream-name . "Biobase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/Biobase") - (synopsis "Base functions for Bioconductor") - (description - "This package provides functions that are needed by many other packages -on Bioconductor or which replace R functions.") - (license license:artistic2.0))) - -(define-public r-annotationdbi - (package - (name "r-annotationdbi") - (version "1.52.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationDbi" version)) - (sha256 - (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) - (properties - `((upstream-name . "AnnotationDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationDbi") - (synopsis "Annotation database interface") - (description - "This package provides user interface and database connection code for -annotation data packages using SQLite data storage.") - (license license:artistic2.0))) - -(define-public r-biomart - (package - (name "r-biomart") - (version "2.46.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biomaRt" version)) - (sha256 - (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) - (properties - `((upstream-name . "biomaRt"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/biomaRt") - (synopsis "Interface to BioMart databases") - (description - "biomaRt provides an interface to a growing collection of databases -implementing the @url{BioMart software suite, http://www.biomart.org}. The -package enables retrieval of large amounts of data in a uniform way without -the need to know the underlying database schemas or write complex SQL queries. -Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, -Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt -users direct access to a diverse set of data and enable a wide range of -powerful online queries from gene annotation to database mining.") - (license license:artistic2.0))) - -(define-public r-biocparallel - (package - (name "r-biocparallel") - (version "1.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocParallel" version)) - (sha256 - (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) - (properties - `((upstream-name . "BiocParallel"))) - (build-system r-build-system) - (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocParallel") - (synopsis "Bioconductor facilities for parallel evaluation") - (description - "This package provides modified versions and novel implementation of -functions for parallel evaluation, tailored to use with Bioconductor -objects.") - (license (list license:gpl2+ license:gpl3+)))) - -(define-public r-biostrings - (package - (name "r-biostrings") - (version "2.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biostrings" version)) - (sha256 - (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) - (properties - `((upstream-name . "Biostrings"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/Biostrings") - (synopsis "String objects and algorithms for biological sequences") - (description - "This package provides memory efficient string containers, string -matching algorithms, and other utilities, for fast manipulation of large -biological sequences or sets of sequences.") - (license license:artistic2.0))) - -(define-public r-rsamtools - (package - (name "r-rsamtools") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Rsamtools" version)) - (sha256 - (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) - (properties - `((upstream-name . "Rsamtools"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") - (synopsis "Interface to samtools, bcftools, and tabix") - (description - "This package provides an interface to the @code{samtools}, -@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence -Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed -tab-delimited (tabix) files.") - (license license:expat))) - -(define-public r-delayedarray - (package - (name "r-delayedarray") - (version "0.16.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedArray" version)) - (sha256 - (base32 - "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) - (properties - `((upstream-name . "DelayedArray"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DelayedArray") - (synopsis "Delayed operations on array-like objects") - (description - "Wrapping an array-like object (typically an on-disk object) in a -@code{DelayedArray} object allows one to perform common array operations on it -without loading the object in memory. In order to reduce memory usage and -optimize performance, operations on the object are either delayed or executed -using a block processing mechanism. Note that this also works on in-memory -array-like objects like @code{DataFrame} objects (typically with Rle columns), -@code{Matrix} objects, and ordinary arrays and data frames.") - (license license:artistic2.0))) - (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") @@ -8045,13 +7751,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.42.2") + (version "1.42.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "17ns5hvx5q8mrmkgb6linspwml62mi34i6al5bxlib5xi9d9f04s")))) + "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) |