From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:33 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:33 +0000 Received: from localhost ([127.0.0.1]:37755 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000IF-HJ for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:32 -0400 Received: from mail-wr1-f44.google.com ([209.85.221.44]:39708) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjS-0000Ao-Qx for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:55 -0400 Received: by mail-wr1-f44.google.com with SMTP id v12so22200534wrq.6 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:54 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=Poe2LuMsCnuZtRINjiEp0jYCsrl+xGyc9hxjLq6OOdE=; b=VtoL3XvQvB+lz02tW1QKmhpRW6gN9Fcpj35Tji1OLCjcT4zJM8TiR9IycOrhTzoU5F cFzJvo/JLPw+U2bo7qzENwxijsxk8YlbSdi2ttKvHcd9eX2QhXlzVTVxiUpZEEmlUZh8 ZEBtUi+Q/IsObwISy4GdvDP925z6ji+GK+vHJ0pa8DVBJM7X3opJuAEUpIf2uwyQKJ3b oNivCA5MCJtEt33v12mMmMVoBhncmVS9HfTd6iyCp6aSBt6gY9j1RVDzogosyurEeDoC wn0NnrkIBirpzT+A3m6rO3GVnuym15DRzfqP1TedV9k19LP3Vgf4M2/0m3XqX2gTLJqU uIxA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=Poe2LuMsCnuZtRINjiEp0jYCsrl+xGyc9hxjLq6OOdE=; b=fl0KnCBC3snu6CVxNn4shTYdEqsL3KJvGrYyFpgjtSHGha8bR4KIPOuEY55k2kAhH3 191qoJWEfcx8UcflZ0rGCAERkLH6l537fiMn64RwwRTWofK6yo0vUZWXcRmuu5yGR8V3 H7lbx5nTjpZGwORV30Xey6DsgPN2enZmi6hmajoUE+edfw75ii4vPCcaAsr9AdsLAdK7 uF1biJZtEym7/ponvfvVkP8xC2oja6DIYnOhKDj98nd23I4iMFXB9p4TPmMeymoKFwYN vhyDoihryuK1l8iCEDRWpMhnMbcsEO3yZyi7+OwBMF0ODLajqVd3jxeRUu8PDyUiIYhg 9cXQ== X-Gm-Message-State: AOAM5317/wBEmSPyi6K9tk9vs1WtSkV2OsQloHjueIvg90vzd/rkPpJw 4DupVywyqG+sA6h0mr5tOay1aiLDaTI= X-Google-Smtp-Source: ABdhPJz2yDVQguBrk3AjLSYO8f1XTzASO11WuQVPq88MVDNRkzEu7INj7HmkdJTl0bHmvf/+Gr3G6g== X-Received: by 2002:adf:fc44:: with SMTP id e4mr11317508wrs.23.1621628809274; Fri, 21 May 2021 13:26:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 31/50] gnu: r-biovizbase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:03 +0200 Message-Id: <20210521202622.26591-31-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 48575 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioinformatics.scm (r-biovizbase): Move from here... * gnu/packages/bioconductor.scm (r-biovizbase): ...to here. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 42 --------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05c4896276..7439ad96da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2044,6 +2044,48 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) + (properties `((upstream-name . "biovizBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dichromat" ,r-dichromat) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +high-level packages for biological data visualization. This saves development +effort and encourages consistency.") + (license license:artistic2.0))) + (define-public r-bsgenome (package (name "r-bsgenome") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 600c2ca81e..e6692ece0c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8979,48 +8979,6 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) -(define-public r-biovizbase - (package - (name "r-biovizbase") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "biovizBase" version)) - (sha256 - (base32 - "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) - (properties `((upstream-name . "biovizBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/biovizBase") - (synopsis "Basic graphic utilities for visualization of genomic data") - (description - "The biovizBase package is designed to provide a set of utilities, color -schemes and conventions for genomic data. It serves as the base for various -high-level packages for biological data visualization. This saves development -effort and encourages consistency.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.30.1