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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:19 +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=B48575.16216288621264 (code B ref 48575); Fri, 21 May 2021 20:28:19 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:42 +0000 Received: from localhost ([127.0.0.1]:37787 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkE-0000KE-9S for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:42 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:44799) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjb-0000Cj-HI for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wm1-f45.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810227wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:03 -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=DcGOzSgQkR2g22Nixp75eN8pMoCurmXHwafY9ehZgaU=; b=Oo+WVjOU8Gw+qDFMJi4ew0yTy+0R1M3QtLUV2OupCL9wMOhjeQ4A3P4Wcwof2Sz/Ud Ats84u87+nLkMOCBXn++nMb1EfzGekcwrYydyRk1ABZftP1srKqi7+73KkQ/khZJJn+d aLwGzR5xPiELpsd6+lwK3+O2VO9fyWDZIarGcpbO4uKTAZq9eJ7oM+4KQ70H2CmjGBoP npxkp3Y5tRq28lBjypvrBmNK0JfhmptmwKwLXJvZWOJjaM2IqbTlRiokRKqYcyIuym4r +MsvK05OSCwzyLt2Io6b/iKSOMj+cewYu1yvfxrJ7f1l5kDwDJVXk7mP8eIb0uIDN7Zr 2Wqw== 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=DcGOzSgQkR2g22Nixp75eN8pMoCurmXHwafY9ehZgaU=; b=nvaW5YnuTAIuzxM9HSTOC5YxJKdN8LEacvBIxeWGdQELA1pCFZPhKjIQx2gHbpRMAG OtEdqza47ak461zbs81PVAnyiyr6uZST3XX24XjzVUY2i0SMfc+YwKjPxXG1hRUQKirj NGHHgHsBPROsvtN8WabQDAY2EQUuqBbbT4uuEZ+GvQgUAiCsPbjwSK4SBuMqMCSTX2FJ 3+DlBxc+Fx5/EHhf+khYGVkXeZfS+p3Pk9L3O6Sy+qO9jpPCLPoGbc3giKEgOvFAaB+f HKv3ReZXeXIpm6NFyXzoS+Qi7nR/SQzNJCV1+pB/jtww0f39gVuJmR4ePUgy8yT7f3Wh /reA== X-Gm-Message-State: AOAM531YZiYlDYYXSaHezWVOctCdlCEhCDhitTFHz3MqV/UBlw7Gl0fI jxi+cUzbauiUn4Lk2/MuXb0fvsWx+HE= X-Google-Smtp-Source: ABdhPJxqy38qqPD+gcg493Sy60TWMyhCqCeIbIwOLmQbosCSoiMZaG9lePlJfoLQ8/MzPoSeWK0WjA== X-Received: by 2002:a05:600c:19c8:: with SMTP id u8mr10555534wmq.25.1621628816978; Fri, 21 May 2021 13:26:56 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:56 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:20 +0200 Message-Id: <20210521202622.26591-48-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-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f224a5ecb4..eee1561c1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.") chromstaR package.") (license license:gpl3))) +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ee3d9d4f3..2acca0c055 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copyhelper - (package - (name "r-copyhelper") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://bioconductor.org/packages/release/" - "data/experiment/src/contrib/CopyhelpeR_" - version ".tar.gz")) - (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) - (properties `((upstream-name . "CopyhelpeR"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/CopyhelpeR/") - (synopsis "Helper files for CopywriteR") - (description - "This package contains the helper files that are required to run the -Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content -and mappability files for the reference genomes hg18, hg19, hg38, mm9 and -mm10. In addition, it contains a blacklist filter to remove regions that -display copy number variation. Files are stored as GRanges objects from the -GenomicRanges Bioconductor package.") - (license license:gpl2))) - (define-public r-copywriter (package (name "r-copywriter")