From patchwork Wed Jan 18 17:35:58 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46273 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BA6DF27BBEB; Wed, 18 Jan 2023 17:37:28 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 53DBB27BBE9 for ; Wed, 18 Jan 2023 17:37:27 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pICNE-0003IS-5L; Wed, 18 Jan 2023 12:37:20 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pICMx-00032H-Df for guix-patches@gnu.org; Wed, 18 Jan 2023 12:37:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pICMw-000224-QE for guix-patches@gnu.org; Wed, 18 Jan 2023 12:37:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pICMw-0008SF-Ca; Wed, 18 Jan 2023 12:37:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60938] [PATCH 1/2] gnu: Add r-breakpointrdata. References: <2098d8d186584816ab54d4bf0fae811b@mdc-berlin.de> In-Reply-To: <2098d8d186584816ab54d4bf0fae811b@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Wed, 18 Jan 2023 17:37:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60938 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60938@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60938-submit@debbugs.gnu.org id=B60938.167406338932415 (code B ref 60938); Wed, 18 Jan 2023 17:37:02 +0000 Received: (at 60938) by debbugs.gnu.org; 18 Jan 2023 17:36:29 +0000 Received: from localhost ([127.0.0.1]:41712 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pICMP-0008Qk-Av for submit@debbugs.gnu.org; Wed, 18 Jan 2023 12:36:29 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:52711) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pICMN-0008QJ-47 for 60938@debbugs.gnu.org; Wed, 18 Jan 2023 12:36:27 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1674063379; x=1675877780; bh=vE5gTP1EW/lRU5R 2qqFSZwXZ0va8sC13Hu+MnpIMwHc=; b=ZO99BLiHpmIsy8ac9sTpiugJSvdUWeV L2ZQr4d+dMagL2zPhVqANmy/NvH0JF48SHIsD5ODmpinzFmI8v6Xdu8wfR+Jz8Xf +o4Esi+ZEdg/3PbCmXUMA18/imOW1wnDzxRwjtN09XyoWaw/bjhz/FC2GbBWCa7n r3jGK+Tp84o0= 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 id A4DA8A00E5 for <60938@debbugs.gnu.org>; Wed, 18 Jan 2023 18:36:19 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Wed, 18 Jan 2023 18:36:19 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Wed, 18 Jan 2023 18:35:58 +0100 Message-ID: <20230118173559.73235-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27394.001 X-TM-AS-Result: No-10--3.156400-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCz1q+x7zkhJWuuLH9BII+4qrKs axUiN/ykX0jceDJtHIX6VxxWFgkHXo8WMkQWv6iV3LAytsQR4e42j49Ftap9Eymsk/wUE4hrfhH cYdCBpji2D2lkFrSm7smtEjvT7qkBBcZmvivayu4km79DsdqtZvZjYKGnywmAqGFSBjIMTrqyd8 QtKiOUiKySI09+jVzKSi32HRIEsm7TnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.156400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27394.001 X-TM-SNTS-SMTP: 6AE0FE38331F459EBF5FB1421F549A6FFC22F8DC38C15B33D98B2273DF982CB72002:F 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-breakpointrdata): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) base-commit: f088763356e88c4911ee933fdafcad6ed66a7aa3 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca236bcf75..27f8111982 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1291,6 +1291,26 @@ (define-public r-biscuiteerdata biscuiteer.") (license license:gpl3))) +(define-public r-breakpointrdata + (package + (name "r-breakpointrdata") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointRdata" version 'experiment)) + (sha256 + (base32 + "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn")))) + (properties `((upstream-name . "breakpointRdata"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/breakpointRdata") + (synopsis "Strand-seq data for demonstration purposes") + (description + "This packpage is a collection of Strand-seq data. The main pupose is to +demonstrate functionalities of breakpointR package.") + (license license:expat))) + (define-public r-celldex (package (name "r-celldex") From patchwork Wed Jan 18 17:35:59 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46274 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 3401F27BBEB; Wed, 18 Jan 2023 17:37:33 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3A85827BBE9 for ; Wed, 18 Jan 2023 17:37:31 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pICNF-0003Rc-ML; Wed, 18 Jan 2023 12:37:21 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pICMz-00032W-VC for guix-patches@gnu.org; Wed, 18 Jan 2023 12:37:13 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pICMx-00022L-6W for guix-patches@gnu.org; Wed, 18 Jan 2023 12:37:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pICMw-0008SN-Oo; Wed, 18 Jan 2023 12:37:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60938] [PATCH 2/2] gnu: Add r-breakpointr. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Wed, 18 Jan 2023 17:37:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60938 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60938@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60938-submit@debbugs.gnu.org id=B60938.167406339032422 (code B ref 60938); Wed, 18 Jan 2023 17:37:02 +0000 Received: (at 60938) by debbugs.gnu.org; 18 Jan 2023 17:36:30 +0000 Received: from localhost ([127.0.0.1]:41714 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pICMP-0008Qm-N2 for submit@debbugs.gnu.org; Wed, 18 Jan 2023 12:36:30 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:43315) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pICMN-0008QN-45 for 60938@debbugs.gnu.org; Wed, 18 Jan 2023 12:36:28 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1674063381; x=1675877782; bh=kBfY2ir2uhCRL1LSd+DUAX7bpGHji930jpv/7GkvmEY=; b=htBewX9fRijm j9hY/fATExsdA70jmWk1dF4G0tbG+W17f/+GitNqAFVfsAUv/ICKN/fAw82qoOG2 WcDlikMBCo769IbV1lJ9QfH7nHOoVxIKZLFLgUtjQJ0PnOH8zIexP7/2VsEi1K9V raA3ZX0+iCf5isq8N8OMyVWhH2Q954w= 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 id 0413FA00FD for <60938@debbugs.gnu.org>; Wed, 18 Jan 2023 18:36:21 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Wed, 18 Jan 2023 18:36:19 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Wed, 18 Jan 2023 18:35:59 +0100 Message-ID: <20230118173559.73235-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230118173559.73235-1-madalinionel.patrascu@mdc-berlin.de> References: <20230118173559.73235-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27394.001 X-TM-AS-Result: No-10--0.413400-5.000000 X-TMASE-MatchedRID: JUGAxiLh1cP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyAkbY6/7arYNrDs9HvnBn1mA0 yITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUYuAaf1pLv9xKwqMwmNxj1CZsd X1PnnWo1L3bM/Y1onuF59N94Ca7QE/2E+UFdM+F9uyfwcit/QGDBjpLMF7xLLLQ5N4Q2X53nQJ8 8ZHP8DjvmJf6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.413400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27394.001 X-TM-SNTS-SMTP: 55672831C7866B206C59CF32332A7223D8DD610454E7CA13237184D0B25DA7B62002:F 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-breakpointr): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 27f8111982..5a69aecf18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3500,6 +3500,40 @@ (define-public r-biocgenerics packages.") (license license:artistic2.0))) +(define-public r-breakpointr + (package + (name "r-breakpointr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointR" version)) + (sha256 + (base32 + "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx")))) + (properties `((upstream-name . "breakpointR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-breakpointrdata + r-cowplot + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/BreakPointR") + (synopsis "Find breakpoints in Strand-seq data") + (description + "This package implements functions for finding breakpoints, plotting and +export of Strand-seq data.") + (license license:expat))) + (define-public r-cardelino (package (name "r-cardelino")