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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681612601 (code B ref 45399); Wed, 23 Dec 2020 18:07:06 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:56 +0000 Received: from localhost ([127.0.0.1]:54098 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XH-0003H3-EY for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:55 -0500 Received: from mail-wr1-f49.google.com ([209.85.221.49]:41830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X9-0003F9-Vo for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:49 -0500 Received: by mail-wr1-f49.google.com with SMTP id a12so44408wrv.8 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:47 -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=peYF/DoNoLu3JFCsZndzO5YP6WEcT8mXxSok6WpQS0Q=; b=Z1xhEEuRaIxSlJWzERkYjCxDf9kj4seg1PyWwKxqeT8iyjUMjNL0kVr2DUKObDRN94 FSKl0jm0fdZsVxeLb/PMApBn3phr3LV5dWe+wBaMIzSYtFBqjL/TpiFl0gOzuazC3FGe 1231qjbWlXCkfGlkf30KAnPGr7Id2V8hnxiJ0SimwJ4k6NKV7iR7j7Vn7vGA0luC1HDJ gMBHHhdKs4VU7KY5JnmsPeMjJoctmfVKk5cIh7fb/gjeBGJEuIZ47hEGnR/aYPMUNSHy eXX9/j8w/Qyi6QzpVOz3L2yOkULy7FBwZ++0j9euiOiRfJ+JP8AUlv71/U9SSiC+krvW m+7A== 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=peYF/DoNoLu3JFCsZndzO5YP6WEcT8mXxSok6WpQS0Q=; b=iVuSrd3mXae4vXkz6sgiITJ+EQwKf01F9zpZY4EyL/fWuNglszCdt13hFfRgKUUpCd XDRxgbdQ4zcErYsoDLMDbJdFoOBEr2NfuwjHX/uodlwmVlT2djq7Mm4iflNyxgrFAKLP FumAs7tk4L8EvLQQhxjVsMd7ASGZ3/T030EiP/oJNw0o9zax6XGxNOjK6wRAWQ83xb0b nc9JDwOF4Vz0bAuWteKfVT5wjXXa0ZfbULXsVkka1Ed+HSwKqzifmNI3EWMYGcp5mP++ Yhf/hgdAIgR91Klqs/I+EW3pbUOzomKOlKDCvFQyK0xCx8aAw/3rNAdhVOhSu+tcge7d WoEA== X-Gm-Message-State: AOAM532rP7RWuVlUOxWz3Rhlqgtpr+hawFSPUvmjokCTCcmiA2TtOuzt MP9q/EzB8boDCQ9bZlxhXcw3Fcl0pBE= X-Google-Smtp-Source: ABdhPJxhEJvkck/aU7Rh2mTlOg/hBUxQAWIh7glJ8y4AxHWDUB0RpxwODQTz1fArFqCw1RRZfoPXuw== X-Received: by 2002:adf:8b4a:: with SMTP id v10mr30616234wra.212.1608746802438; Wed, 23 Dec 2020 10:06:42 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:42 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:32 +0100 Message-Id: <20201223180635.58647-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-Spam-Score: 2.77 Authentication-Results: aspmx1.migadu.com; dkim=fail (headers rsa verify failed) header.d=gmail.com header.s=20161025 header.b=Z1xhEEuR; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 0073E9404D5 X-Spam-Score: 2.77 X-Migadu-Scanner: scn1.migadu.com X-TUID: hxfeJCFS+AzS * gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here... * gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here. Replace 'string-append' by 'bioconductor-uri' with 'annotation'. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 27 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 466bb71101..3b8dce30e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-homo-sapiens + (package + (name "r-homo-sapiens") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Homo.sapiens" version 'annotation)) + (sha256 + (base32 + "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) + (properties + `((upstream-name . "Homo.sapiens"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) + ("r-organismdbi" ,r-organismdbi) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/Homo.sapiens/") + (synopsis "Annotation package for the Homo.sapiens object") + (description + "This package contains the Homo.sapiens object to access data from +several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c59d7a690..2a6ac38505 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10623,38 +10623,6 @@ and more.") the earlier snpMatrix package, allowing for uncertainty in genotypes.") (license license:gpl3))) -(define-public r-homo-sapiens - (package - (name "r-homo-sapiens") - (version "1.3.1") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "Homo.sapiens_" - version ".tar.gz")) - (sha256 - (base32 - "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) - (properties - `((upstream-name . "Homo.sapiens"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/Homo.sapiens/") - (synopsis "Annotation package for the Homo.sapiens object") - (description - "This package contains the Homo.sapiens object to access data from -several related annotation packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2