From unknown Sat Jun 14 03:53:19 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45873] [PATCH] gnu: Add r-snapatac. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 14 Jan 2021 19:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 45873 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45873@debbugs.gnu.org Cc: rekado@elephly.net, =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.161065430419568 (code B ref -1); Thu, 14 Jan 2021 19:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 14 Jan 2021 19:58:24 +0000 Received: from localhost ([127.0.0.1]:39372 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l08lA-00055U-72 for submit@debbugs.gnu.org; Thu, 14 Jan 2021 14:58:23 -0500 Received: from lists.gnu.org ([209.51.188.17]:34740) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l08l6-00055K-6W for submit@debbugs.gnu.org; Thu, 14 Jan 2021 14:58:18 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:49450) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l08l4-0005f6-No for guix-patches@gnu.org; Thu, 14 Jan 2021 14:58:15 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36965) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l08kz-000628-8o for guix-patches@gnu.org; Thu, 14 Jan 2021 14:58:14 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 229ADA00CD; Thu, 14 Jan 2021 20:58:05 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1610654284; x=1612468685; bh=azIILlLbta2zED5aFbmTlfhHp6vctNkTKRsbVgfAvyU=; b=Z3ayiUQAMlUb jzMxGanv2Ds8tM0wiA7hn8ZV8Fd1oZUufNwwiA1XBXdyArN5t/VdkIDbxojN39xv whLeeXVsmIwj1n9qYG3zT5Kk8NlNXfTI2DAp5+ZRx75oGL0YvfSsiQfttNIIoZYs mYc0rajbHodUWOpR+m0K3D8KrJBJ0IY= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 2TUwVRnvFWAZ; Thu, 14 Jan 2021 20:58:04 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS; Thu, 14 Jan 2021 20:58:04 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2106.2; Thu, 14 Jan 2021 20:58:04 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Thu, 14 Jan 2021 20:57:44 +0100 Message-ID: <20210114195744.15053-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-25912.002 X-TM-AS-Result: No-10--0.384400-8.000000 X-TMASE-MatchedRID: 4ppMg0uMmAzRtBxlwMMWfD8Ckw9b/GFeTJDl9FKHbrmv/7fHaEp6E4qU frHU7PyNoSAZDASoRXAkrgMnNPRaLnS86kHFizFwUYXhMajr0x70IUHuSVWDh55GLlvTiXrYiMD 6wB/IizLsR+687/f48oPJHXL3hk5Z+5T6zKmlZhdcDXoTHAPnrEPIlAqA4/DEfyjNXlbBvnSgWc ErZpkOROVGjmZbJjjRj7CjdbsFOivybSXiGX6jItrZIypbofP1ojX2kLuehY2r2AvucEN0g5K1t EWloVFzDf1TH3R7beV5OPD8XJFfpL9ZdlL8eonaC24oEZ6SpSmcfuxsiY4QFF0Rqxdnqz72iLF+ KL0OzGfFDrXi9ku1Fo/kryjCBAbcgDvqJ+TsXTT2s+z39Q7BAevNMiGrMEPD9fta5byLM/Kf8ul AQx3Zb2/H7LhIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.384400-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-25912.002 X-TM-SNTS-SMTP: E9E9D413116B0D971337DD31C86CBEB652D0ECFD72CB63362F4C9FF9632810572000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * 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 ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -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 From unknown Sat Jun 14 03:53:19 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45873] [PATCH] gnu: Add r-snapatac. References: <20210114195744.15053-1-madalinionel.patrascu@mdc-berlin.de> In-Reply-To: <20210114195744.15053-1-madalinionel.patrascu@mdc-berlin.de> Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 14 Jan 2021 23:44:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45873 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45873@debbugs.gnu.org Cc: "Patrascu, Madalin Ionel" Received: via spool by 45873-submit@debbugs.gnu.org id=B45873.16106678378208 (code B ref 45873); Thu, 14 Jan 2021 23:44:01 +0000 Received: (at 45873) by debbugs.gnu.org; 14 Jan 2021 23:43:57 +0000 Received: from localhost ([127.0.0.1]:39592 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l0CHU-00028J-CR for submit@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 ) id 1l0CHR-000289-6Y for 45873@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@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1610667830; s=zoho; d=elephly.net; i=rekado@elephly.net; 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 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@elephly.net> 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" 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 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 19 17:16:32 2021 Received: (at control) by debbugs.gnu.org; 19 Mar 2021 21:16:32 +0000 Received: from localhost ([127.0.0.1]:51130 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lNMTv-0006wg-VY for submit@debbugs.gnu.org; Fri, 19 Mar 2021 17:16:32 -0400 Received: from eggs.gnu.org ([209.51.188.92]:36400) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lNMTu-0006r8-0E for control@debbugs.gnu.org; Fri, 19 Mar 2021 17:16:30 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:43649) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lNMTo-00087w-Sf for control@debbugs.gnu.org; Fri, 19 Mar 2021 17:16:24 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=59482 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lNMTo-0003iw-C2 for control@debbugs.gnu.org; Fri, 19 Mar 2021 17:16:24 -0400 Date: Fri, 19 Mar 2021 22:16:23 +0100 Message-Id: <87mtuyc09k.fsf@gnu.org> To: control@debbugs.gnu.org From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: control message for bug #45873 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) tags 45873 + moreinfo quit From unknown Sat Jun 14 03:53:19 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45873] [PATCH] gnu: Add r-snapatac. Resent-From: Simon Tournier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Feb 2025 22:17:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45873 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch moreinfo To: Ricardo Wurmus Cc: 45873@debbugs.gnu.org, "Patrascu, Madalin Ionel" Received: via spool by 45873-submit@debbugs.gnu.org id=B45873.174017620328199 (code B ref 45873); Fri, 21 Feb 2025 22:17:06 +0000 Received: (at 45873) by debbugs.gnu.org; 21 Feb 2025 22:16:43 +0000 Received: from localhost ([127.0.0.1]:39101 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tlbK7-0007Kf-C5 for submit@debbugs.gnu.org; Fri, 21 Feb 2025 17:16:43 -0500 Received: from mail-wm1-x334.google.com ([2a00:1450:4864:20::334]:54425) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1tlbJz-0007IF-Av for 45873@debbugs.gnu.org; Fri, 21 Feb 2025 17:16:36 -0500 Received: by mail-wm1-x334.google.com with SMTP id 5b1f17b1804b1-43948f77f1aso16108195e9.0 for <45873@debbugs.gnu.org>; Fri, 21 Feb 2025 14:16:35 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1740176189; x=1740780989; darn=debbugs.gnu.org; h=mime-version:user-agent:message-id:date:references:in-reply-to :subject:cc:to:from:from:to:cc:subject:date:message-id:reply-to; bh=IN/9nPY5AiVDE4Ec9hZsnHR20CcsT8pLeQ708nfh86o=; b=UZ9ug+OYsr6/mffoXNDRg/Do0wvYacT/lgoVTm0NKos1+rpUFzFstklbsmVszjEokB PAW1V2EKVr9cMBL9bmVDNaB7FiKlNE5U1mwtHk1CVTaWCA8Oe/0/z+yZvGBcMgnTxdgY j/0R1wwz9xGHkXWoyaohevAnOUet04NUkQZkeR8HVGXKtmLe0atLFKDkJL+kRR7phvzc lzgb9SWGWHGDNntLlj3tuKTDJRoop4G9aRGN0TwigLmzO3dNxeb42sVAN3j/fDzRGCRl 0F+csMyAHiqsx7ZU/7FC5lu9nqNsyG9/l4qIVp2OVXZyqONbx+SGBVQhkVPimvaqjWcf ZXhw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1740176189; x=1740780989; h=mime-version:user-agent:message-id:date:references:in-reply-to :subject:cc:to:from:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=IN/9nPY5AiVDE4Ec9hZsnHR20CcsT8pLeQ708nfh86o=; b=K5lLdXD1QlVRPRNnOQH6aLDrNzq1Ky6VVJfiZly4MABH6Txpmc569Gib6t1dm/tYoh a169xC3BGLuCD92Eswhx5ch9EnD+MFsmiqeYQBMXAGgeYvazsRcqbLZDpzXTmZwc1qM5 vi1cgilwVqlYffWcudsFrk/5TBOTkICugeEjbEl9Ihr3g33zRoFQKxD4xHVrttqkMN7U stt2wzPJKnzEyU1SN+QzfLJWneVOHtaecdaBoG7qIUwrC0ru29ZsiJ5uv9zVlI0+oUYs bvnI1X2y8Zjc1KWu+tZlB96O0AU57NAKgOzaRVc6XDWCTfHl41bCBYuei5ZZzq6cb811 thYg== X-Gm-Message-State: AOJu0YzQQwG3IhHsuo39bdZAzhFvC/3PZ+BN7ch0LiRzx0pnA+dhO4or /GBgAszTMKmIQeVEtiITNyup+x6bf2InAjMgDOqv+nDp7ulZeZxUTohutUY3 X-Gm-Gg: ASbGncvQgVHwR09gX+vv0TRbD5xRshX0WHTkWYIBuMedokL+7tq+Hqq9gdvIy62sOho 6C7O9QZ7EjkxYUAQ12kHnLverIwGeJB+Lj/pNZl/5YguxP9aUzCpQLkCkqjDC358QpagAguhk/x oxbI/cWW+dlLV3IsIileWKowQX0pMMHu0AhQ1TKB/C1bhYwZdaNpn/z4NEL38IX3ZMlJAHgFD92 lEK6Ceu43Y+Y/z4e2L9OwxidT/Rirj4YamyB2TBQyxIKX1Qo6Dpk9PMzlIgQN3WGCXWp5HbxOMR pPNxHMTJ78Wu3OX/qbY11Jk= X-Google-Smtp-Source: AGHT+IEmPJxJ1EybhHyVVxS6IWvzCi3BUTqmq7gRLCkDaZrMrG7rvwAaDsdl/lznhLqmTzsT7adgNQ== X-Received: by 2002:a05:600c:458e:b0:439:8340:637 with SMTP id 5b1f17b1804b1-439ae21e4c8mr49871915e9.30.1740176189134; Fri, 21 Feb 2025 14:16:29 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:1306:e65:4f3d:4de8]) by smtp.gmail.com with ESMTPSA id 5b1f17b1804b1-439b02ce37fsm30150235e9.8.2025.02.21.14.16.28 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 Feb 2025 14:16:28 -0800 (PST) From: Simon Tournier In-Reply-To: <87bldrccem.fsf@elephly.net> (Ricardo Wurmus's message of "Fri, 15 Jan 2021 00:43:45 +0100") References: <20210114195744.15053-1-madalinionel.patrascu@mdc-berlin.de> <87bldrccem.fsf@elephly.net> Date: Fri, 21 Feb 2025 23:13:25 +0100 Message-ID: <8734g7eyka.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Ricardo, Madalin, Thanks for the submission. For reference of this old submission: https://issues.guix.gnu.org/issue/45873 On Fri, 15 Jan 2021 at 00:43, Ricardo Wurmus wrote: > 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? Well, what is the status? Is it still relevant? Or closing? Cheers, simon