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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
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
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To: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
Subject: bug#76793: closed ([PATCH] gnu: Add sickle.)
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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
--
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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
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Navid Afkhami <navid.afkhami@HIDDEN> skribis:
> * gnu/packages/bioinformatics.scm (sickle): New variable.
>
> Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8
Applied, thank you!
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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>
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Date: Mon, 10 Mar 2025 13:35:02 +0000
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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
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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
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Navid Afkhami <navid.afkhami@HIDDEN> skribis:
> * gnu/packages/bioinformatics.scm (sickle): New variable.
>
> Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8
Applied, thank you!
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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
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