From unknown Sun Jun 22 07:52:47 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#62989] [PATCH] gnu: Add python-rseqc. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Apr 2023 10:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 62989 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 62989@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.168207296517776 (code B ref -1); Fri, 21 Apr 2023 10:30:02 +0000 Received: (at submit) by debbugs.gnu.org; 21 Apr 2023 10:29:25 +0000 Received: from localhost ([127.0.0.1]:39429 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppo16-0004ce-ID for submit@debbugs.gnu.org; Fri, 21 Apr 2023 06:29:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:48766) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppo14-0004cV-CE for submit@debbugs.gnu.org; Fri, 21 Apr 2023 06:29:23 -0400 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 1ppo13-0004zj-1M for guix-patches@gnu.org; Fri, 21 Apr 2023 06:29:21 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ppo10-0004lZ-7T for guix-patches@gnu.org; Fri, 21 Apr 2023 06:29:20 -0400 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=1682072945; x=1683887346; bh=tHAvQ9r16Mt/4KI lz0atmE1UI15ADAJU1GktMGULK2c=; b=TldhiV8huc17S+1NzcVew93Lm3aVj4h rLikZeUEZgw2pFUgzkFA3+LHnYcSZMqPLMVLSURkJ/GWFrqqxOMsCD6oGxFp8Knj Y1N2mmTkVxyDh+wimSMYV2YPtNugb9l9Q3VvyieWTEiBpEcxG6zJGZLor/41G9Ba /1bzj1HajZpM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1DBC23001C1 for ; Fri, 21 Apr 2023 12:29:04 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.23; Fri, 21 Apr 2023 12:28:53 +0200 From: Navid Afkhami Date: Fri, 21 Apr 2023 10:28:45 +0000 Message-ID: <20230421102845.46529-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.007 X-TM-AS-Result: No-10--3.154000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v//j4ZByyZz4qY5ZGw7wyeHkZC 5B+W0s+ORXZ1NN5BDL+y49GTXfURFvPvhbFNrEFPdCok3ibXlQQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYVzsLn+s6Pt3EXTA9Aa7TJd1ArEckgw08d0F4zJ9WbGHdL/W +8em8C4tyqEsXAzv4sLYlA6xHfI7qlc7EzRuCJbO/3KtoK3huDX7GF+64huyLjmNKuuvgamoYI1 erIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.154000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.007 X-TM-SNTS-SMTP: 9C2DAB0C5EA244BF9F2024692C027A5454D9B6138847C8F162A70EAF77D630CB2002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 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 (python-rseqc): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b27e12a5b4..ecc1815539 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3060,6 +3060,30 @@ (define-public python-pysam also includes an interface for tabix.") (license license:expat))) +(define-public python-rseqc + (package + (name "python-rseqc") + (version "5.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "RSeQC" version)) + (sha256 + (base32 + "106av4ms6agrfjdlw5j3fsrk86clr0f4ygysv19g66l6hj3laz9w")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-bx-python python-numpy python-pybigwig + python-pysam)) + (native-inputs (list python-cython python-nose)) + (home-page "https://github.com/MonashBioinformaticsPlatform/RSeQC") + (synopsis "RNA-seq quality control packag") + (description + "Useful modules that can comprehensively evaluate high throughput sequence data. +Some basic modules quickly inspect sequence, quality, nucleotide composition bias, +PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, +mapped reads distribution, coverage uniformity, strand specificity, transcript level +RNA integrity and etc.") + (license license:gpl3))) + (define-public python-twobitreader (package (name "python-twobitreader") -- 2.34.1 From unknown Sun Jun 22 07:52:47 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#62989: closed ([PATCH] gnu: Add python-rseqc.) Message-ID: References: <87jzu96uwb.fsf@elephly.net> <20230421102845.46529-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 62989 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 62989@debbugs.gnu.org Date: Sat, 05 Aug 2023 21:30:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1691271002-30080-1" This is a multi-part message in MIME format... ------------=_1691271002-30080-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #62989: [PATCH] gnu: Add python-rseqc. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 62989@debbugs.gnu.org. --=20 62989: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D62989 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1691271002-30080-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 62989-done) by debbugs.gnu.org; 5 Aug 2023 21:29:04 +0000 Received: from localhost ([127.0.0.1]:58272 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSOpc-0007ne-KV for submit@debbugs.gnu.org; Sat, 05 Aug 2023 17:29:04 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21728) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSOpY-0007nC-8y for 62989-done@debbugs.gnu.org; Sat, 05 Aug 2023 17:29:03 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1691270938; cv=none; d=zohomail.com; s=zohoarc; b=cNlF8dJYaZ8XDV/0e40/vm7ISTNHMdkpcdQ5SvjvbTLT4VUNz4QUNZK+NGdKt9GVkDW0AFQMyvfeSPdqox4DJ4I+Cn4USzjt+oXMLdFDeTUKZUg3cUic7VTpgGKG/Infg7smv12wha4HEePupQeVfeTl1HUQtfdP5hrJhH34e3M= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1691270938; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=62+fg5kTNgyssFtpUMZ7+8X0R3xQzqjtMGnXBQqXCBU=; b=nI/XjSqjKyTMvY2vCFr7Gm70MhDKUJS+1N64gD28+Q8SZ5pYQbVO7aJtImkb3GVB35I/AVIQVb37sc+GyD8PuiEXVBXoQkfEkksilbP976qFOwieZ5yWMqnC0bJyb4RzMDwaEWJTndnRLZZOVNNnCctWcLr151+KW3FiLZuagsA= 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= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1691270938; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=62+fg5kTNgyssFtpUMZ7+8X0R3xQzqjtMGnXBQqXCBU=; b=L5TIFMdjpCpJRSOE4SCjJIl+2ZerQR0e/rzSJ/3x2RSZ8mGJRtlV9fk/wPw7omf+ OytQA1FvF9/y16bGTN6hr46WTBn+n2kBm708eUwcL2C+PYZbCPX699tHGEZUu+qLZUa NX1+w+eZ4cAa/Aj78xXBoLfl1LXCMtxcqHQITHb0= Received: from localhost (193-109-142-46.pool.kielnet.net [46.142.109.193]) by mx.zohomail.com with SMTPS id 1691270936444286.9811320675582; Sat, 5 Aug 2023 14:28:56 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 62989-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-rseqc. Date: Sat, 05 Aug 2023 23:27:23 +0200 Message-ID: <87jzu96uwb.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-Debbugs-Envelope-To: 62989-done 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 (-) I=E2=80=99m closing this because 1. we have a package for rseqc. 2. this is an unmaintained fork 3. IIRC it doesn=E2=80=99t actually work --=20 Ricardo ------------=_1691271002-30080-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 21 Apr 2023 10:29:25 +0000 Received: from localhost ([127.0.0.1]:39429 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppo16-0004ce-ID for submit@debbugs.gnu.org; Fri, 21 Apr 2023 06:29:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:48766) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppo14-0004cV-CE for submit@debbugs.gnu.org; Fri, 21 Apr 2023 06:29:23 -0400 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 1ppo13-0004zj-1M for guix-patches@gnu.org; Fri, 21 Apr 2023 06:29:21 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ppo10-0004lZ-7T for guix-patches@gnu.org; Fri, 21 Apr 2023 06:29:20 -0400 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=1682072945; x=1683887346; bh=tHAvQ9r16Mt/4KI lz0atmE1UI15ADAJU1GktMGULK2c=; b=TldhiV8huc17S+1NzcVew93Lm3aVj4h rLikZeUEZgw2pFUgzkFA3+LHnYcSZMqPLMVLSURkJ/GWFrqqxOMsCD6oGxFp8Knj Y1N2mmTkVxyDh+wimSMYV2YPtNugb9l9Q3VvyieWTEiBpEcxG6zJGZLor/41G9Ba /1bzj1HajZpM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1DBC23001C1 for ; Fri, 21 Apr 2023 12:29:04 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.23; Fri, 21 Apr 2023 12:28:53 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-rseqc. Date: Fri, 21 Apr 2023 10:28:45 +0000 Message-ID: <20230421102845.46529-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.007 X-TM-AS-Result: No-10--3.154000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v//j4ZByyZz4qY5ZGw7wyeHkZC 5B+W0s+ORXZ1NN5BDL+y49GTXfURFvPvhbFNrEFPdCok3ibXlQQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYVzsLn+s6Pt3EXTA9Aa7TJd1ArEckgw08d0F4zJ9WbGHdL/W +8em8C4tyqEsXAzv4sLYlA6xHfI7qlc7EzRuCJbO/3KtoK3huDX7GF+64huyLjmNKuuvgamoYI1 erIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.154000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.007 X-TM-SNTS-SMTP: 9C2DAB0C5EA244BF9F2024692C027A5454D9B6138847C8F162A70EAF77D630CB2002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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 (python-rseqc): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b27e12a5b4..ecc1815539 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3060,6 +3060,30 @@ (define-public python-pysam also includes an interface for tabix.") (license license:expat))) +(define-public python-rseqc + (package + (name "python-rseqc") + (version "5.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "RSeQC" version)) + (sha256 + (base32 + "106av4ms6agrfjdlw5j3fsrk86clr0f4ygysv19g66l6hj3laz9w")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-bx-python python-numpy python-pybigwig + python-pysam)) + (native-inputs (list python-cython python-nose)) + (home-page "https://github.com/MonashBioinformaticsPlatform/RSeQC") + (synopsis "RNA-seq quality control packag") + (description + "Useful modules that can comprehensively evaluate high throughput sequence data. +Some basic modules quickly inspect sequence, quality, nucleotide composition bias, +PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, +mapped reads distribution, coverage uniformity, strand specificity, transcript level +RNA integrity and etc.") + (license license:gpl3))) + (define-public python-twobitreader (package (name "python-twobitreader") -- 2.34.1 ------------=_1691271002-30080-1--