From debbugs-submit-bounces@debbugs.gnu.org Fri May 21 16:27:36 2021 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:36 +0000 Received: from localhost ([127.0.0.1]:37773 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk8-0000JJ-4Z for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:36 -0400 Received: from mail-wm1-f41.google.com ([209.85.128.41]:55106) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjY-0000By-DO for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:07 -0400 Received: by mail-wm1-f41.google.com with SMTP id o127so11748717wmo.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:00 -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=PZLbfIvxLq/mL2OJh+TE+U0x2EZDlIdOz60SG+/jzmY=; b=Kw/WiLO701QvTdsRAd7kafxJq8Zf8ml2+ADA32oN4JXTbslCS0sz291v5umHrT4ff5 nOlz19mEqOtAxqfLxIsxdUet2szaaKkeJmfevJbXiCAU6ZoZx6TtqDziEcpjSIg85wlU pPu497IXQHDBL1r1DMLBRipVuyRO2QNjp+k0ygpyTzYxcje5qpGfwuKd4yun1zETilBA gXv7c2munhqWxl4QeV65bMVBlXadKZVEWF7r3crDdxxUeHQEQOrnO9SF6z6pI2PQL8Ao gK8uWA632qGA7YxnCK3UV2pBUR8BvHwQ36zYpLUElhKYkTUiDQfVbLu6lm7rzq1KeXct 4twA== 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=PZLbfIvxLq/mL2OJh+TE+U0x2EZDlIdOz60SG+/jzmY=; b=l4w0qaaMWHxKk1ZmF5PxbjRWNarnQ6KlPlH5rRMWOEuG+7XAkcjT0TdopI7aCpDRor aEpUyS/N8T80ltanyJeQsv+edwzsCTAu4wx9rHeL9iqQpOHg+fGUjg22KAIVc9O4ZAVu /kBn4GZ6/RKU8G/yzQKoN+SC03M3BJE/RF+2hmGvI9lqVT6bIaxU0IMB5/PZW4PiRBQ3 0IAYGKUtNbNE5yoYilC/MErIdhCit66uY+7q4OsSFnInj8NEBO0PMwuUd3dROrIGY9Kx FhyNrNJ7dY72E1SKavjXC23sfw6CXG7FDv4Gv335PUCT0pF0rxNFBnVYyUFVfc6Igcrd yHmg== X-Gm-Message-State: AOAM5332rqSVWVxH/Y035yDkGsIonOGVIDnSDt7qElRImobgHlW6UraJ /9Ac7v9JWGI44pnz3wxb5t/cvsUBk+k= X-Google-Smtp-Source: ABdhPJwfZSvxFXfwr1NfZoiOQlG0I2nBTsd4STGusgGPg8BEBFZOc1Tpr1Nk9LRvbRMJ9fbjUCVoUw== X-Received: by 2002:a7b:c446:: with SMTP id l6mr10424299wmi.75.1621628813742; Fri, 21 May 2021 13:26:53 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:53 -0700 (PDT) From: zimoun To: 48575@debbugs.gnu.org. Subject: [PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:13 +0200 Message-Id: <20210521202622.26591-41-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-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 99607ba564..1d38fa1c05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3307,6 +3307,55 @@ proteomics packages.") the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas + (package + (name "r-rcas") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RCAS" version)) + (sha256 + (base32 + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) + (properties `((upstream-name . "RCAS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) + ("r-pbapply" ,r-pbapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-plotrix" ,r-plotrix) + ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-s4vectors" ,r-s4vectors) + ("pandoc" ,pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae61ecae74..a1ee4b6772 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,55 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rcas - (package - (name "r-rcas") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "RCAS" version)) - (sha256 - (base32 - "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) - (properties `((upstream-name . "RCAS"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (synopsis "RNA-centric annotation system") - (description - "RCAS aims to be a standalone RNA-centric annotation system that provides -intuitive reports and publication-ready graphics. This package provides the R -library implementing most of the pipeline's features.") - (home-page "https://github.com/BIMSBbioinfo/RCAS") - (license license:artistic2.0))) - (define-public rcas-web (package (name "rcas-web") -- 2.30.1