From unknown Sat Aug 09 05:05:48 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#76793] [PATCH] gnu: Add sickle. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 06 Mar 2025 23:37:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 76793 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76793@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.174130416318310 (code B ref -1); Thu, 06 Mar 2025 23:37:02 +0000 Received: (at submit) by debbugs.gnu.org; 6 Mar 2025 23:36:03 +0000 Received: from localhost ([127.0.0.1]:45873 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tqKl1-0004lG-3f for submit@debbugs.gnu.org; Thu, 06 Mar 2025 18:36:03 -0500 Received: from lists.gnu.org ([2001:470:142::17]:43678) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tqKky-0004kh-Gb for submit@debbugs.gnu.org; Thu, 06 Mar 2025 18:36:01 -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 1tqKks-0008Hc-0b for guix-patches@gnu.org; Thu, 06 Mar 2025 18:35:54 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tqKkn-0000Ef-Cv for guix-patches@gnu.org; Thu, 06 Mar 2025 18:35:53 -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=1741304145; x=1743118546; bh=R23j8OYv4E0tuod 2M7v2SiApOnHhI1BUS1QlFrebSDs=; b=E24il6yxj3M0vwucwweaRQCYqIFiJvf 7JetTxE/MvYkgMGgE+Zhv3BcsCTpc0YeA2AymHuFr6UbSzOBdBkaXKkOBhmvrXVi NEDxr27g7y6qCr2VVPzHgDxJ7LPNSKHSSD7bzRt40THA4VUN0iSs1ihzTusegP5l bG38GhdPUaGA= 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 2EB9D448C93 for ; Fri, 7 Mar 2025 00:35:45 +0100 (CET) Received: from localhost (141.80.121.83) 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 15.2.1544.14; Fri, 7 Mar 2025 00:35:44 +0100 From: Navid Afkhami Date: Thu, 6 Mar 2025 23:35:38 +0000 Message-ID: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.43.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.121.83] 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-14.0.0.3223-9.1.2019-29034.003 X-TM-AS-Result: No-10--6.815000-5.000000 X-TMASE-MatchedRID: LWf8uVYp425YhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJPABo6AR1sb2oqKGmXzWdcHju2XlcEx9HQGj5QT3EuXhtVwVFL7iTibmUn DtXkHJ7CQ2a12fXt6M04cL3v000r64tfbBzctauIpUHxp0N9ilXDFNDSVd5IswFMWRKmWW+BQzE Z/XFnH2zYImz0YWdqXb2VwDsAgdqVTRCwidbD/AeT5AnjO7TXt9VRkPJa+sq4Pm15xyht8lVvII d8M26gTOfEmq6feyfOHJGU+Wm68bpsI6K9TYesL+uN81tKRKmila73bcvT9XofNKVVMSZEfFE6O Yw+bHaMcuPaxUU6RtU5rw7fiOo2cYDttQUGqHZU= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.815000-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-29034.003 X-TM-SNTS-SMTP: 8AF112DE8A8B48BD4D24B1C49985038433C412672873E2E7AD4FA7B0E2C4A5922000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@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, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, RCVD_IN_VALIDITY_SAFE_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioinformatics.scm (sickle): New variable. Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8 --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f7f39f525d..0129b9ebeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14542,6 +14542,40 @@ (define-public shorah frequency of the different genetic variants present in a mixed sample.") (license license:gpl3+))) +(define-public sickle + (package + (name "sickle") + (version "1.33") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/najoshi/sickle") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bnq480lpylq9sfsa1y71b4qz0ipi2zjnp8ds48fh10ijlwmwmdc")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "sickle" + (string-append #$output "/bin"))))))) + (propagated-inputs (list zlib)) + (home-page "https://github.com/najoshi/sickle") + (synopsis "Adaptive trimming tool for FASTQ files using quality") + (description + "Sickle is a tool that trims reads based on quality and length thresholds. +It uses sliding windows to detect low-quality bases at the 3'-end and +high-quality bases at the 5'-end. Additionally, it discards reads based +on the length threshold.") + (license license:expat))) + (define-public ruby-bio-kseq (package (name "ruby-bio-kseq") base-commit: 1f26b0eec83b5dc949900a743ed01088cb093c65 -- 2.43.0 From unknown Sat Aug 09 05:05:48 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#76793: closed (Re: [bug#76793] [PATCH] gnu: Add sickle.) Message-ID: References: <87bju9rouo.fsf@gnu.org> <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 76793 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 76793@debbugs.gnu.org Date: Mon, 10 Mar 2025 13:35:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1741613702-21146-1" This is a multi-part message in MIME format... ------------=_1741613702-21146-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #76793: [PATCH] gnu: Add sickle. 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 76793@debbugs.gnu.org. --=20 76793: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D76793 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1741613702-21146-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 76793-done) by debbugs.gnu.org; 10 Mar 2025 13:34:52 +0000 Received: from localhost ([127.0.0.1]:36727 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trdHP-0005Ua-SZ for submit@debbugs.gnu.org; Mon, 10 Mar 2025 09:34:52 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:34462) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trdHM-0005UG-4I for 76793-done@debbugs.gnu.org; Mon, 10 Mar 2025 09:34:48 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 1AFF11D7; Mon, 10 Mar 2025 14:34:42 +0100 (CET) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id VKDcYT8TO5kA; Mon, 10 Mar 2025 14:34:41 +0100 (CET) Received: from ribbon (unknown [193.50.110.159]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 6983E1C2; Mon, 10 Mar 2025 14:34:40 +0100 (CET) From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Navid Afkhami Subject: Re: [bug#76793] [PATCH] gnu: Add sickle. In-Reply-To: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de> (Navid Afkhami's message of "Thu, 6 Mar 2025 23:35:38 +0000") References: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de> Date: Mon, 10 Mar 2025 14:34:39 +0100 Message-ID: <87bju9rouo.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain X-Rspamd-Server: hera X-Rspamd-Queue-Id: 1AFF11D7 X-Spamd-Result: default: False [5.24 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(2.79)[0.929]; R_MIXED_CHARSET(0.56)[subject]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_TWO(0.00)[2]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; MID_RHS_MATCH_FROM(0.00)[] X-Spamd-Bar: +++++ X-Rspamd-Action: greylist X-Spam-Level: ***** X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 76793-done Cc: 76793-done@debbugs.gnu.org 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: -0.0 (/) Navid Afkhami skribis: > * gnu/packages/bioinformatics.scm (sickle): New variable. > > Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8 Applied, thank you! ------------=_1741613702-21146-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 6 Mar 2025 23:36:03 +0000 Received: from localhost ([127.0.0.1]:45873 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tqKl1-0004lG-3f for submit@debbugs.gnu.org; Thu, 06 Mar 2025 18:36:03 -0500 Received: from lists.gnu.org ([2001:470:142::17]:43678) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tqKky-0004kh-Gb for submit@debbugs.gnu.org; Thu, 06 Mar 2025 18:36:01 -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 1tqKks-0008Hc-0b for guix-patches@gnu.org; Thu, 06 Mar 2025 18:35:54 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tqKkn-0000Ef-Cv for guix-patches@gnu.org; Thu, 06 Mar 2025 18:35:53 -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=1741304145; x=1743118546; bh=R23j8OYv4E0tuod 2M7v2SiApOnHhI1BUS1QlFrebSDs=; b=E24il6yxj3M0vwucwweaRQCYqIFiJvf 7JetTxE/MvYkgMGgE+Zhv3BcsCTpc0YeA2AymHuFr6UbSzOBdBkaXKkOBhmvrXVi NEDxr27g7y6qCr2VVPzHgDxJ7LPNSKHSSD7bzRt40THA4VUN0iSs1ihzTusegP5l bG38GhdPUaGA= 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 2EB9D448C93 for ; Fri, 7 Mar 2025 00:35:45 +0100 (CET) Received: from localhost (141.80.121.83) 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 15.2.1544.14; Fri, 7 Mar 2025 00:35:44 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add sickle. Date: Thu, 6 Mar 2025 23:35:38 +0000 Message-ID: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.43.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.121.83] 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-14.0.0.3223-9.1.2019-29034.003 X-TM-AS-Result: No-10--6.815000-5.000000 X-TMASE-MatchedRID: LWf8uVYp425YhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJPABo6AR1sb2oqKGmXzWdcHju2XlcEx9HQGj5QT3EuXhtVwVFL7iTibmUn DtXkHJ7CQ2a12fXt6M04cL3v000r64tfbBzctauIpUHxp0N9ilXDFNDSVd5IswFMWRKmWW+BQzE Z/XFnH2zYImz0YWdqXb2VwDsAgdqVTRCwidbD/AeT5AnjO7TXt9VRkPJa+sq4Pm15xyht8lVvII d8M26gTOfEmq6feyfOHJGU+Wm68bpsI6K9TYesL+uN81tKRKmila73bcvT9XofNKVVMSZEfFE6O Yw+bHaMcuPaxUU6RtU5rw7fiOo2cYDttQUGqHZU= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.815000-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-29034.003 X-TM-SNTS-SMTP: 8AF112DE8A8B48BD4D24B1C49985038433C412672873E2E7AD4FA7B0E2C4A5922000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@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, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, RCVD_IN_VALIDITY_SAFE_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioinformatics.scm (sickle): New variable. Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8 --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f7f39f525d..0129b9ebeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14542,6 +14542,40 @@ (define-public shorah frequency of the different genetic variants present in a mixed sample.") (license license:gpl3+))) +(define-public sickle + (package + (name "sickle") + (version "1.33") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/najoshi/sickle") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bnq480lpylq9sfsa1y71b4qz0ipi2zjnp8ds48fh10ijlwmwmdc")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "sickle" + (string-append #$output "/bin"))))))) + (propagated-inputs (list zlib)) + (home-page "https://github.com/najoshi/sickle") + (synopsis "Adaptive trimming tool for FASTQ files using quality") + (description + "Sickle is a tool that trims reads based on quality and length thresholds. +It uses sliding windows to detect low-quality bases at the 3'-end and +high-quality bases at the 5'-end. Additionally, it discards reads based +on the length threshold.") + (license license:expat))) + (define-public ruby-bio-kseq (package (name "ruby-bio-kseq") base-commit: 1f26b0eec83b5dc949900a743ed01088cb093c65 -- 2.43.0 ------------=_1741613702-21146-1--