Ludovic Courtès <ludo@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.Received: (at 45873) by debbugs.gnu.org; 14 Jan 2021 23:43:57 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Jan 14 18:43:57 2021 Received: from localhost ([127.0.0.1]:39592 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1l0CHU-00028J-CR for submit <at> debbugs.gnu.org; Thu, 14 Jan 2021 18:43:57 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21104) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1l0CHR-000289-6Y for 45873 <at> debbugs.gnu.org; Thu, 14 Jan 2021 18:43:54 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1610667830; cv=none; d=zohomail.com; s=zohoarc; b=jjCdTKHS4wBGN4iyH9ahlaIXodbjGftPDpLBA9LnCNCmMLDDz5zLkbpuwIvNmKt8oqAVnMEgTltTovl/8VtF+1Yr1hIiZ25eGQEnwF17ORDcgOkabYeEgusM6W4rVJGL/IWMSBB/ud8Ic/DGmaopVxtSbElxHx4azxchskpSOXI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1610667830; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:MIME-Version:Message-ID:Subject:To; bh=MmlPVJiws6YpSBSLAE+mqQ+50/E4cEo05mah/FE1hlA=; b=NNOuwh4aBGtDjvbL3jOViL+Sysvjt6XNaX367wA/+NbFdLXvfcYEj/iT3EMrTk4wGrqZ7zIUTfivLfxHKHE3Y4IrtsKWoONNMoDsLNoqpvWxEKRBO5KnQOYP24bFutCzsWR49+J+TS1IxA4oh4lz7WelCv8HHIXsZoaTiCHH69o= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1610667830; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=MmlPVJiws6YpSBSLAE+mqQ+50/E4cEo05mah/FE1hlA=; b=FoxDYcKyAlYvClSJ3vanN6H1AieJmfiziqneKol64GlmhmvRq5/wQOkX5c5fAGLc bbq3SHZLRYnh16BEwSGj8XOtju16VEoAt3BpJJn6cSYxgaFqwm3kZrsEQgobF+qbqF1 POq6VpHd8n68acayPnOmIpsBiZ58BjZpB5eRAe4U= Received: from localhost (p54ad4ef9.dip0.t-ipconnect.de [84.173.78.249]) by mx.zohomail.com with SMTPS id 1610667828528795.7766630830127; Thu, 14 Jan 2021 15:43:48 -0800 (PST) User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus <rekado@HIDDEN> To: 45873 <at> debbugs.gnu.org Subject: [PATCH] gnu: Add r-snapatac. X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 15 Jan 2021 00:43:45 +0100 Message-ID: <87bldrccem.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 45873 Cc: "Patrascu, Madalin Ionel" <MadalinIonel.Patrascu@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi Madalin, thanks for the patch. It looks good to me but I have a few questions. The README file claims that the Python Snaptools must be installed. This package does not do this, so I suppose the package will fail when it=E2=80=99s run in an environment that does not have the Snaptools on the = PATH. Do you happen to have a package definition for the Snaptools as well, so that we could either propagate it or patch r-snapatac to retain references to the executables it provides? I also see references to Homer and other bioinfo tools, which are not provided by this package and which are not found among the inputs. Does it make sense to install this package when these tools are not available? --=20 Ricardo
guix-patches@HIDDEN:bug#45873; Package guix-patches.
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To: <guix-patches@HIDDEN>
Subject: [PATCH] gnu: Add r-snapatac.
Date: Thu, 14 Jan 2021 20:57:44 +0100
Message-ID: <20210114195744.15053-1-madalinionel.patrascu@HIDDEN>
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* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
---
gnu/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++++++++-
1 file changed, 50 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 512abcd8fd..6be82773ac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,7 +11,7 @@
;;; Copyright © 2017 Arun Isaac <arunisaac@HIDDEN>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@HIDDEN>
;;; Copyright © 2018 Gábor Boskovits <boskovits@HIDDEN>
-;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>
+;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>
;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@HIDDEN>
;;; Copyright © 2019 Brian Leung <bkleung89@HIDDEN>
;;; Copyright © 2019 Brett Gilio <brettg@HIDDEN>
@@ -7073,6 +7073,55 @@ sequence.")
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
+(define-public r-snapatac
+ (package
+ (name "r-snapatac")
+ (version "2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/r3fang/SnapATAC")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av"))))
+ (properties `((upstream-name . "SnapATAC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bigmemory" ,r-bigmemory)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dosnow" ,r-dosnow)
+ ("r-edger" ,r-edger)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-irlba" ,r-irlba)
+ ("r-matrix" ,r-matrix)
+ ("r-plyr" ,r-plyr)
+ ("r-plot3d" ,r-plot3d)
+ ("r-rann" ,r-rann)
+ ("r-raster" ,r-raster)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/r3fang/SnapATAC")
+ (synopsis "Single nucleus analysis package for ATAC-Seq")
+ (description
+ "This package provides a fast and accurate analysis toolkit for single
+cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing).
+Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and
+reveal cell-type specific regulatory landscapes. However, the exceeding data
+sparsity has posed unique challenges for the data analysis. This package
+@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large-
+scale single cell ATAC-seq data which includes quality control, normalization,
+clustering analysis, differential analysis, motif inference and exploration of
+single cell ATAC-seq sequencing data.")
+ (license license:gpl3)))
+
(define-public r-scde
(package
(name "r-scde")
--
2.30.0
Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#45873; Package guix-patches.
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