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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:08 +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=B45399.160874681612616 (code B ref 45399); Wed, 23 Dec 2020 18:07:08 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:56 +0000 Received: from localhost ([127.0.0.1]:54102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XI-0003HJ-9s for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:56 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:55673) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XB-0003FD-5y for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:49 -0500 Received: by mail-wm1-f51.google.com with SMTP id c124so169565wma.5 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:49 -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=JIXZfPUyUUvVrjc3l7vPUDsnSQFk0ZTymAngTOU/cLg=; b=b7ufJbaOzI4V9Fw9zRYRr+akAdm3bjG1f82SFVEInWlcLuI4WPwoz+jqiAElDvzHNv Xn9Hj9+55NYfklCHQ/fB7Z6FbVZO9kTU8vOuYC/fhCHdhiwM5tRwOTFRc3VuiH05UOW+ +feYEf/0irPzqbMUVgrCOECbgvWZhEniZ9j35gzBxhfY5ksW1ECko1eDQe1llu+KaoJ1 nQukfQXNlp1UDynC1IcbgUQDPB+9BOc+G274i7lqRJENM1hf1NfkfjY+nxDSh5doEOzi lTGVBp1oYHmtcnPcHiHPYsL2pZW410NjwjMkYAm9/PHNtupYToTOobH5tZUp5voAWVqK Apvw== 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=JIXZfPUyUUvVrjc3l7vPUDsnSQFk0ZTymAngTOU/cLg=; b=UTQEDkWd1wP4bAn3PtaayBu27n339GdstduYVUVMaBdBGc5fQAEfz8gD3DF9LYmTsO KWhkEbMqix0vWQHPzEQlihw6AIXg4id6+tWLNXg/KgzadjWj9MUg5+itZc9+dFDFrET3 xfR595QC9M4JVzZhLre3Jh8SJ+Eu3+/1HqqYZcmpDAO1Xv9uTfLWzaJ0UYC7fZs57US0 QmIQVosbMg62bm9uZ+ImUZz/Ju+b2qet6LqWOtl+2M7a0aM461iwdvJKzoAzbBsi9Cup UgcGFYSPdU80WQYaeXWfrJ6/7A02RXNvTTukUmFWizXSv2UdQIglG3QtoZ4ZTmfZLujV JiMg== X-Gm-Message-State: AOAM531VoTfqIj2jjz1MI5ddcjVoN/Bhwn65UkKf/OEMcc+xWLvzJJic m3DGxBJ3OdtPMMoPVhcWWHRTjwjPrqg= X-Google-Smtp-Source: ABdhPJwjo8H4boqqqeFuEYrxpHpxpuKBXh9PcKDUrLCnk6H8pWK5DcbgzD6ypv2w0TEtS888Amctdg== X-Received: by 2002:a7b:cd91:: with SMTP id y17mr767072wmj.171.1608746803662; Wed, 23 Dec 2020 10:06:43 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:43 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:34 +0100 Message-Id: <20201223180635.58647-10-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=b7ufJbaO; 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: 60EAA940480 X-Spam-Score: 2.77 X-Migadu-Scanner: scn1.migadu.com X-TUID: 4Qa8gGQIfYJj * gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 --------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff9e26bbde..a3dd93e763 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) +(define-public r-gqtlbase + (package + (name "r-gqtlbase") + (version "1.21.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLBase" version)) + (sha256 + (base32 + "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) + (properties `((upstream-name . "gQTLBase"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This is an upstream bug. + (add-after 'unpack 'fix-imports + (lambda _ + (substitute* "NAMESPACE" + ((".*maxffmode.*") "") + (("importFrom\\(ff,.*") "import(ff)\n")) + #t))))) + (propagated-inputs + `(("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-biocgenerics" ,r-biocgenerics) + ("r-bit" ,r-bit) + ("r-doparallel" ,r-doparallel) + ("r-ff" ,r-ff) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLBase") + (synopsis "Infrastructure for eQTL, mQTL and similar studies") + (description + "The purpose of this package is to simplify the storage and interrogation +of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, +and more.") + (license license:artistic2.0))) + (define-public r-gqtlstats (package (name "r-gqtlstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 76236929de..bc483e6f13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10549,53 +10549,6 @@ views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.") (license license:artistic2.0))) -(define-public r-gqtlbase - (package - (name "r-gqtlbase") - (version "1.21.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLBase" version)) - (sha256 - (base32 - "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) - (properties `((upstream-name . "gQTLBase"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This is an upstream bug. - (add-after 'unpack 'fix-imports - (lambda _ - (substitute* "NAMESPACE" - ((".*maxffmode.*") "") - (("importFrom\\(ff,.*") "import(ff)\n")) - #t))))) - (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLBase") - (synopsis "Infrastructure for eQTL, mQTL and similar studies") - (description - "The purpose of this package is to simplify the storage and interrogation -of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, -and more.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2