X-Loop: help-debbugs@HIDDEN Subject: [bug#76793] [PATCH] gnu: Add sickle. 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envelope-from=Navid.Afkhami@HIDDEN; 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 <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> 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
Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) Content-Type: text/plain; charset=utf-8 X-Loop: help-debbugs@HIDDEN From: help-debbugs@HIDDEN (GNU bug Tracking System) To: Navid Afkhami <navid.afkhami@HIDDEN> Subject: bug#76793: Acknowledgement ([PATCH] gnu: Add sickle.) Message-ID: <handler.76793.B.174130416318310.ack <at> debbugs.gnu.org> References: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> X-Gnu-PR-Message: ack 76793 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 76793 <at> debbugs.gnu.org Date: Thu, 06 Mar 2025 23:37:02 +0000 Thank you for filing a new bug report with debbugs.gnu.org. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. Your message has been sent to the package maintainer(s): guix-patches@HIDDEN If you wish to submit further information on this problem, please send it to 76793 <at> debbugs.gnu.org. Please do not send mail to help-debbugs@HIDDEN unless you wish to report a problem with the Bug-tracking system. --=20 76793: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D76793 GNU Bug Tracking System Contact help-debbugs@HIDDEN with problems
MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@HIDDEN From: help-debbugs@HIDDEN (GNU bug Tracking System) To: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN> Subject: bug#76793: closed ([PATCH] gnu: Add sickle.) CC: tracker <at> debbugs.gnu.org Message-ID: <handler.76793.D76793.174161369221120.ackdone <at> debbugs.gnu.org> References: <87bju9rouo.fsf@HIDDEN> <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> X-Gnu-PR-Message: closed 76793 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Date: Mon, 10 Mar 2025 13:35:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1741613701-21146-0" This is a multi-part message in MIME format... ------------=_1741613701-21146-0 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Your message dated Mon, 10 Mar 2025 14:34:39 +0100 with message-id <87bju9rouo.fsf@HIDDEN> and subject line Re: [bug#76793] [PATCH] gnu: Add sickle. has caused the debbugs.gnu.org bug report #76793, regarding [PATCH] gnu: Add sickle. to be marked as done. (If you believe you have received this mail in error, please contact help-debbugs@HIDDEN) --=20 76793: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D76793 GNU Bug Tracking System Contact help-debbugs@HIDDEN with problems ------------=_1741613701-21146-0 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 <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tqKl1-0004lG-3f for submit <at> 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 <Navid.Afkhami@HIDDEN>) id 1tqKky-0004kh-Gb for submit <at> 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 <Navid.Afkhami@HIDDEN>) id 1tqKks-0008Hc-0b for guix-patches@HIDDEN; 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 <Navid.Afkhami@HIDDEN>) id 1tqKkn-0000Ef-Cv for guix-patches@HIDDEN; 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 <guix-patches@HIDDEN>; 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 <navid.afkhami@HIDDEN> To: <guix-patches@HIDDEN> Subject: [PATCH] gnu: Add sickle. 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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 ------------=_1741613701-21146-0 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 <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1trdHP-0005Ua-SZ for submit <at> 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 <ludo@HIDDEN>) id 1trdHM-0005UG-4I for 76793-done <at> 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?= <ludo@HIDDEN> To: Navid Afkhami <navid.afkhami@HIDDEN> Subject: Re: [bug#76793] [PATCH] gnu: Add sickle. In-Reply-To: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> (Navid Afkhami's message of "Thu, 6 Mar 2025 23:35:38 +0000") References: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> Date: Mon, 10 Mar 2025 14:34:39 +0100 Message-ID: <87bju9rouo.fsf@HIDDEN> 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 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.0 (/) Navid Afkhami <navid.afkhami@HIDDEN> skribis: > * gnu/packages/bioinformatics.scm (sickle): New variable. > > Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8 Applied, thank you! ------------=_1741613701-21146-0--
MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@HIDDEN From: help-debbugs@HIDDEN (GNU bug Tracking System) To: Navid Afkhami <navid.afkhami@HIDDEN> Subject: bug#76793: closed (Re: [bug#76793] [PATCH] gnu: Add sickle.) Message-ID: <handler.76793.D76793.174161369221120.notifdone <at> debbugs.gnu.org> References: <87bju9rouo.fsf@HIDDEN> <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> X-Gnu-PR-Message: they-closed 76793 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 76793 <at> 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 <at> debbugs.gnu.org. --=20 76793: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D76793 GNU Bug Tracking System Contact help-debbugs@HIDDEN 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 <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1trdHP-0005Ua-SZ for submit <at> 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 <ludo@HIDDEN>) id 1trdHM-0005UG-4I for 76793-done <at> 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?= <ludo@HIDDEN> To: Navid Afkhami <navid.afkhami@HIDDEN> Subject: Re: [bug#76793] [PATCH] gnu: Add sickle. In-Reply-To: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> (Navid Afkhami's message of "Thu, 6 Mar 2025 23:35:38 +0000") References: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> Date: Mon, 10 Mar 2025 14:34:39 +0100 Message-ID: <87bju9rouo.fsf@HIDDEN> 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 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.0 (/) Navid Afkhami <navid.afkhami@HIDDEN> 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 <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tqKl1-0004lG-3f for submit <at> 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 <Navid.Afkhami@HIDDEN>) id 1tqKky-0004kh-Gb for submit <at> 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 <Navid.Afkhami@HIDDEN>) id 1tqKks-0008Hc-0b for guix-patches@HIDDEN; 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 <Navid.Afkhami@HIDDEN>) id 1tqKkn-0000Ef-Cv for guix-patches@HIDDEN; 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 <guix-patches@HIDDEN>; 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 <navid.afkhami@HIDDEN> To: <guix-patches@HIDDEN> Subject: [PATCH] gnu: Add sickle. Date: Thu, 6 Mar 2025 23:35:38 +0000 Message-ID: <70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@HIDDEN> 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@HIDDEN; 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 <navid.afkhami@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> 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--
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