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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522631010304 (code B ref 47010); Mon, 08 Mar 2021 17:59:05 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:30 +0000 Received: from localhost ([127.0.0.1]:44773 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9F-0002g2-Pb for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:30 -0500 Received: from mail-wr1-f47.google.com ([209.85.221.47]:35336) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9B-0002eK-Ty for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:26 -0500 Received: by mail-wr1-f47.google.com with SMTP id l12so12415752wry.2 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:25 -0800 (PST) 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=qTG2WYw8O0RVcetU4sk65HmZE3LBPPAxun/yQIaIFJI=; b=s14W27df3fNJMO+bvRtr2UpursykI2lkX2QdSs1QXwFFs2KxwGPJUOTSYqzMamfnlj any0cQhay7Av2jiP8Pm82Hy50hQ+aS8XCaKfjyzzJPop64Lu2ob6qUWSSHPXLMHVXjHV HAaX/13gXWnznpIqg8lc60hEn3NsWAF9UDScVlbl4k32Isizfl+oz98+KJBnJoJEyYCA dcq4qvCas9HYcqnUuLgGfsPQ99PfEkNWYkXLjPBrhFoWcb+5syK7ldn+sD3Ne7A+anoS G6RGLLzrKJ/amu97/4UsxnLPMk5WtAF08LnaSd+YRdU573Owq6fIaJgHUDk9m/xz395O PRhw== 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=qTG2WYw8O0RVcetU4sk65HmZE3LBPPAxun/yQIaIFJI=; b=fedIzlWvj8mW4aR0nuEOcAcxzw1aahC7P4nFPMLHz2Re/JcAjzP67sdM7UAaaun15x j9bz6p0ohs76q/f61oXGajqWZOFFjbQcKzXfHP6sVPIk5bh5epFxVZ+czlEOEDFoMoEN pE+JnNfPy3EqWWAbgdTaZH3uEQkKyKlZ0IAq0pEMA2mVnw6Z/4cxLo5i+vubQ8u9F5zQ VZ0bq5Uf/vy34Hsc6beSB/8ttfhTeJRjklG+RdIA9Rz27gp3NJV8/D5EHVkTMoG7uEkj sKdpiiMzUK76cD+UYx3lvjITHaipnpjaZD2VpOfnSgGisBud6R6lPNmV28J3AxXUwP7H vDuQ== X-Gm-Message-State: AOAM531QGQYLPIHED0kiBP/wvZ2burzOZPR83g2D+ylRqhDxfbmLbE9C 5THVIPQb2JWtwZB2od63MiIlNRGk2zg= X-Google-Smtp-Source: ABdhPJzRfy2mNzk67fE+ukzrzh4/AbTMUg2/uh3vhU66itQwHr0wqlAwU4P+fm8l9rn/h4sxIjcOXQ== X-Received: by 2002:a5d:404f:: with SMTP id w15mr25207479wrp.106.1615226300344; Mon, 08 Mar 2021 09:58:20 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:20 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:58:02 +0100 Message-Id: <20210308175802.62517-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f4088db27..05077b422e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (properties `((upstream-name . "ShortRead"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ShortRead") + (synopsis "FASTQ input and manipulation tools") + (description + "This package implements sampling, iteration, and input of FASTQ files. +It includes functions for filtering and trimming reads, and for generating a +quality assessment report. Data are represented as +@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of +purposes. The package also contains legacy support for early single-end, +ungapped alignment formats.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 186b051865..fda4516052 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,49 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-shortread - (package - (name "r-shortread") - (version "1.48.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ShortRead" version)) - (sha256 - (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) - (properties `((upstream-name . "ShortRead"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/ShortRead") - (synopsis "FASTQ input and manipulation tools") - (description - "This package implements sampling, iteration, and input of FASTQ files. -It includes functions for filtering and trimming reads, and for generating a -quality assessment report. Data are represented as -@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of -purposes. The package also contains legacy support for early single-end, -ungapped alignment formats.") - (license license:artistic2.0))) - (define-public r-systempiper (package (name "r-systempiper")