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Mon, 18 Nov 2019 18:22:45 +0100 (CET) Received: from SW-IT-P-CAS3.mdc-berlin.net (mgw10-3.mdc-berlin.de [141.80.113.58]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Mon, 18 Nov 2019 18:22:44 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS3.mdc-berlin.net (141.80.113.58) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 18 Nov 2019 18:22:44 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 18 Nov 2019 18:22:16 +0100 Message-ID: <20191118172216.21813-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25052.000 X-TM-AS-Result: No-3.580700-8.000000-10 X-TMASE-MatchedRID: aQJ0g3G0xD+4WGh1vUSL/3ycvC6I0dJIS1zwNuiBtITfUZT83lbkEA2o 6ebnCAbg09C7KD0jIx5De7JiJBQl19FbcK5rmPO1OVoNrnTEUFrIEQTlh1/QMatkcxxU6EVIeyY Rtv+ZW85LVtcjSeah83NERYbQXfHtY4zV0YEQAfZNP1m95I8DFeJNcHLvRNpEEEQaSVu4yLi+1l 2jbBu0KP75956eQfQ/pA12q7wOhpdKGzvueD4sBnYZxYoZm58FXVlxHIm91HKXBXaJoB9JZ4MbH 85DUZXygMf23PO6/W/6C0ePs7A07ba607moR85RA0p4Wyuc8kpEfJnIWW63f3QwVf/VFjzeugq5 r7LDVAX63KRI3ft6Q39RgtVRvXoUtD0YUK6Ijn0feOyS4eTgy5/QhV1TbGIhh/iXdbS1V7u7j2r WxYQLt0cGnllPWffhN10+4fC3tMDFhXMjdQIJpg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.580700-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25052.000 X-TM-SNTS-SMTP: 5C9E1D0B27BF51704709E8C9DBF13A62A551668E1A3B8B56FA60652AB5894F1B2000:9 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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-harmony): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 07c70fb82c..5da95d66a6 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 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; @@ -15349,3 +15349,39 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public r-harmony + (let ((commit "1a6d77aae524a08a2ca91737a152ab2047ccee78") + (revision "1")) + (package + (name "r-harmony") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/harmony.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1905qsbl5iv3kxki73gmyzshyb8zc6asdaymywndscn7mjkwm7aw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppprogress" ,r-rcppprogress) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/immunogenomics/harmony.git") + (synopsis "Fast, sensitive, and accurate integration of single cell data") + (description + "Harmony software is the R implementation of the algorithm with the same +name for single cell integration, described in Korsunsky et al 2018. Package +includes a standalone Harmony function and interfaces to external frameworks.") + (license license:gpl3))))