From patchwork Fri May 21 20:25:34 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29471 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 3908F27BC81; Fri, 21 May 2021 21:30:27 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B392327BC78 for ; Fri, 21 May 2021 21:30:26 +0100 (BST) Received: from localhost ([::1]:40310 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBmr-0007yW-PB for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:30:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52092) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBjd-0002TX-Un for guix-patches@gnu.org; Fri, 21 May 2021 16:27:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54381) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBjc-0002lI-F5 for guix-patches@gnu.org; Fri, 21 May 2021 16:27:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBja-0000DH-B8 for guix-patches@gnu.org; Fri, 21 May 2021 16:27:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.1621628805580 (code B ref 48575); Fri, 21 May 2021 20:27:02 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:26:45 +0000 Received: from localhost ([127.0.0.1]:37649 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjH-000096-Tj for submit@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:39491) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjF-00008Q-V5 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:42 -0400 Received: by mail-wm1-f47.google.com with SMTP id l18-20020a1ced120000b029014c1adff1edso8057876wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:41 -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=inGeYZj0MDxOj43IPCPKwqIAqrdVVP4wDO7eEwCkZ9Y=; b=FUcfrdV+yKtMZYQVXqc/vRIilL4loO66KJJ4VcP5yZDMmFQ2YAhQ+vqJU/eyUAkpAB 3cWi1RC2wCiNsf7TNnazkDlqc/FldZVNwN8KqXNi3JDw9gbbBj5CjAyY5hXZLr6yPpIZ hs2/Tne2s8cma3DpHvmZ+RkdgmPKKMQcWGvfkXAdw5YpdPVNffBtUrNRDa4MO5fDSvRn CNkSHSNAIT+ml9C7xMze02ZsVVf3qWd0MhVUjZov6bm8O6rwtLpDmtM0zWuLwXWCBJfP kcmk+12vKX2VjhNcmOIE9M4yR+4EGdi1uQaDZfBX0W+e5u/tU75rfnT1fA/lFYQJs7jI vCjw== 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=inGeYZj0MDxOj43IPCPKwqIAqrdVVP4wDO7eEwCkZ9Y=; b=DAm5iG5D7NGZZzWUe2s/4VZj8+qjQbdHgKsn+sS9Rz4Xlx00m2UKtJjXbp5aYZ1dgR a9FvehZhYsjfhUUwt42OgXkXA+SkQVySaLYbpe6VHntivnQslEBFYDhCucdky2kDJvLA 9vn5h4XPFSyDLAYLnHXjnGC33wJg1oOwyHGkFrXg38GA/tfOZeC7oHAM7kWa2ACG4vP4 4JhspuRbK2yc65uvBku8Y9Wkwxyd47jD8LHTARQ0hbQ5329ayP5nybuFVXL8P2wvpeNC xZ/tm6BmsK1zZn8vDtgTijOeRpyrjY5ryYNZrqBUcZq7FZJppqSn0h4CVlwl1KMHN2RR HJKw== X-Gm-Message-State: AOAM530Qqop1I0IpOkpEzuLH9UB5lphhKEtnYRw2OvJS9ABN4MC5BCMK 2YCpUIzrb1R6i9OodFM5eQG9/8HOj88= X-Google-Smtp-Source: ABdhPJzz4ragkfLu+u+L5x3CarlIBBcKBMX5jnt4ZUIes996vvSCjPW97/PcMp3ANW5rKyjRid8NKA== X-Received: by 2002:a7b:c93a:: with SMTP id h26mr10664035wml.141.1621628796349; Fri, 21 May 2021 13:26:36 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.35 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:36 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:34 +0200 Message-Id: <20210521202622.26591-2-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 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-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 --------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f4ff82ad0..42a3d1fffc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + (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))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0d0fe1df30..9fb46c0d5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer - (package - (name "r-rtracklayer") - (version "1.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rtracklayer" version)) - (sha256 - (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) - (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))))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/rtracklayer") - (synopsis "R interface to genome browsers and their annotation tracks") - (description - "rtracklayer is an extensible framework for interacting with multiple -genome browsers (currently UCSC built-in) and manipulating annotation tracks -in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit -built-in). The user may export/import tracks to/from the supported browsers, -as well as query and modify the browser state, such as the current viewport.") - (license license:artistic2.0))) - (define-public r-genomicfeatures (package (name "r-genomicfeatures")