;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de>
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages bioconductor)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #:use-module (guix utils)
  #:use-module (guix git-download)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages chemistry)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages docker)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages ghostscript)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages haskell-xyz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages java)
  #:use-module (gnu packages javascript)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
  #:use-module (gnu packages python)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages tex)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module ((srfi srfi-1) #:hide (zip)))


;;; Annotations

(define-public r-bsgenome-drerio-ucsc-danrer7
  (package
    (name "r-bsgenome-drerio-ucsc-danrer7")
    (version "1.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer7" version
                              'annotation))
       (sha256
        (base32 "17x3hj08jag05y8q4aziy455jy15dpwkdbh97v3byzcda0kpwbpg"))))
    (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer7")))
    (build-system r-build-system)
    (propagated-inputs (list r-bsgenome))
    (home-page
     "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer7")
    (synopsis "Full genome sequences for Danio rerio (UCSC version danRer7)")
    (description
     "This package provides full genome sequences for Danio rerio (Zebrafish)
as provided by UCSC (@code{danRer7}, Jul. 2010) and stored in Biostrings
objects.")
    (license license:artistic2.0)))

(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
  (package
    (name "r-bsgenome-hsapiens-ucsc-hg38-masked")
    (version "1.4.5")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
                              'annotation))
       (sha256
        (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
    (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
    (build-system r-build-system)
    (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
                             r-genomeinfodb))
    (home-page
     "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
    (synopsis
     "Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
    (description
     "This package provides the complete genome sequences for Homo sapiens as
provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
of them has the 4 following masks on top:

@enumerate
@item the mask of assembly gaps (AGAPS mask);
@item the mask of intra-contig ambiguities (AMB mask);
@item the mask of repeats from @code{RepeatMasker} (RM mask);
@item the mask of repeats from Tandem Repeats Finder (TRF mask).
@end enumerate

Only the AGAPS and AMB masks are \"active\" by default.  The sequences are stored
in @code{MaskedDNAString} objects.")
    (license license:artistic2.0)))

(define-public r-ensdb-hsapiens-v79
  (package
    (name "r-ensdb-hsapiens-v79")
    (version "2.99.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "EnsDb.Hsapiens.v79" version
                              'annotation))
       (sha256
        (base32 "0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg"))))
    (properties `((upstream-name . "EnsDb.Hsapiens.v79")))
    (build-system r-build-system)
    (propagated-inputs (list r-ensembldb))
    (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v79")
    (synopsis "Ensembl based annotation package")
    (description "This package exposes an annotation database generated from
Ensembl.")
    (license license:artistic2.0)))

(define-public r-genomewidesnp6crlmm
  (package
    (name "r-genomewidesnp6crlmm")
    (version "1.0.7")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "genomewidesnp6Crlmm" version
                              'annotation))
       (sha256
        (base32 "16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"))))
    (properties `((upstream-name . "genomewidesnp6Crlmm")))
    (