Received: (at 76793-done) by debbugs.gnu.org; 10 Mar 2025 13:34:52 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Mar 10 09:34:52 2025 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!
Navid Afkhami <navid.afkhami@HIDDEN>:Ludovic Courtès <ludo@HIDDEN>:
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From: Navid Afkhami <navid.afkhami@HIDDEN>
To: <guix-patches@HIDDEN>
Subject: [PATCH] gnu: Add sickle.
Date: Thu, 6 Mar 2025 23:35:38 +0000
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* 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
Navid Afkhami <navid.afkhami@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#76793; Package guix-patches.
Full text available.
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