diff mbox series

[bug#76793] gnu: Add sickle.

Message ID 70924564a87dc4e97219e65779eb7226c7d66b1d.1741304137.git.navid.afkhami@mdc-berlin.de
State New
Headers
Series [bug#76793] gnu: Add sickle. |

Commit Message

Navid Afkhami March 6, 2025, 11:35 p.m. UTC 
  * gnu/packages/bioinformatics.scm (sickle): New variable.

Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)


base-commit: 1f26b0eec83b5dc949900a743ed01088cb093c65

Comments

Ludovic Courtès March 10, 2025, 1:34 p.m. UTC | #1 
Navid Afkhami <navid.afkhami@mdc-berlin.de> skribis:

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

Applied, thank you!
diff mbox series

Patch

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")