From patchwork Fri May 21 20:26:04 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29497 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 B1A4C27BC81; Fri, 21 May 2021 21:33:41 +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 3588B27BC78 for ; Fri, 21 May 2021 21:33:41 +0100 (BST) Received: from localhost ([::1]:47000 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBq0-0004Li-FZ for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:33:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52558) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkj-0004uz-Ka for guix-patches@gnu.org; Fri, 21 May 2021 16:28:13 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54509) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkj-000311-C0 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:13 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkj-0000Oa-8e for guix-patches@gnu.org; Fri, 21 May 2021 16:28:13 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 32/50] gnu: r-ensembldb: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:13 +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=B48575.16216288531149 (code B ref 48575); Fri, 21 May 2021 20:28:13 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:33 +0000 Received: from localhost ([127.0.0.1]:37757 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000IM-VH for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:33 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:36550) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjT-0000B0-5B for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:55 -0400 Received: by mail-wm1-f53.google.com with SMTP id n17-20020a7bc5d10000b0290169edfadac9so8084535wmk.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:55 -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=b1fQ4jXDRH91NBR1YEwu2AtIWNrQnr2UAXjU+EigkvE=; b=dEFYgRnFA6i8h2yh0rRAHNyKXqad0m/qRMeboIULxK4NuPDvgqHylql+tkcemeEGsB 1Mtch8SW4PO8C0TCx6Vounrl8UZpK9s2PoOsDW84A628+Z8h1cYKMZP5HWOR0pI75lKW j/CLibR+hnN6f1Ma8xK/BSy3gV9aatt4j0rMtrpy0xd2EelkfD6ST2Nc+FcobfvITcHH /YaUAK60FSJ896nxRbnKE+f7PeEVNJhwUOENQ4n8sBjJx00732heXe3TVHaZfC8Oq+Vy RQCOYsnWiZEgN6m+vMMNavh/qZt+GL3ovzyYOe2pZEjsypey55We19PDqFldGWxOJ6fX aVnw== 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=b1fQ4jXDRH91NBR1YEwu2AtIWNrQnr2UAXjU+EigkvE=; b=K/omwVTyUyP7VHyaRhlczSYstNdCLOQ31aw3BTJ0GSY3acNwLTmOJS3yEuxhwASXMM 8uOqUUPk820QbTPuakDCaZxBjCcRGbzL1HGR2FR1fqhyVm6CtTB7ov5x+8SMq/fNnwaI DYqx4B5VzDNqGpgRLzOPDRwJpx2l8HolMJ7n0Rs8Nid+TotQNDGwpMvDN6I9Q+d6VSgC IEBw6foGjf9ekcn+Rumb4KKPGmRIx1xTboDBEWIVjqHgw0eBin8H61n5Q479szF1+0Ek 3eX3ejIffYyoJnJ7vIN1ytbcAK83cnUBHXZuv4smeSmgElNxmdbMjXpfsMBkCpjYrera 9QDg== X-Gm-Message-State: AOAM5302kunLwRvv+W437ADP5KjaZpYc3CC5tfbqusUVCDxry9HNYKTh v+N9OS7INEymuWlv5CMKFIWkCAFmaRU= X-Google-Smtp-Source: ABdhPJzjmHBVEuBT6sY0d9DYCVr+yZv9fsKajzeGNiW0C/4qYmsD3eJ/JuGcqkWs+vf467y3vD/doA== X-Received: by 2002:a1c:7c03:: with SMTP id x3mr10835339wmc.168.1621628809696; 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.27.2021.05.21.13.26.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:04 +0200 Message-Id: <20210521202622.26591-32-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-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7439ad96da..7e86af7d21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-fastseg (package (name "r-fastseg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6692ece0c..baef88cd2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb - (package - (name "r-ensembldb") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ensembldb" version)) - (sha256 - (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/jotsetung/ensembldb") - (synopsis "Utilities to create and use Ensembl-based annotation databases") - (description - "The package provides functions to create and use transcript-centric -annotation databases/packages. The annotation for the databases are directly -fetched from Ensembl using their Perl API. The functionality and data is -similar to that of the TxDb packages from the @code{GenomicFeatures} package, -but, in addition to retrieve all gene/transcript models and annotations from -the database, the @code{ensembldb} package also provides a filter framework -allowing to retrieve annotations for specific entries like genes encoded on a -chromosome region or transcript models of lincRNA genes.") - ;; No version specified - (license license:lgpl3+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))