GNU bug report logs - #76793
[PATCH] gnu: Add sickle.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: bug#76793: closed (Re: [bug#76793] [PATCH] gnu: Add sickle.)
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.

-- 
76793: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=76793
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ludovic Courtès <ludo <at> gnu.org>
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Cc: 76793-done <at> debbugs.gnu.org
Subject: Re: [bug#76793] [PATCH] gnu: Add sickle.
Date: Mon, 10 Mar 2025 14:34:39 +0100

Navid Afkhami <navid.afkhami <at> mdc-berlin.de> skribis:

> * gnu/packages/bioinformatics.scm (sickle): New variable.
>
> Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8

Applied, thank you!

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add sickle.
Date: Thu, 6 Mar 2025 23:35:38 +0000

* 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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