From 1eda883414947c1c7da187bab13ebe109207dce4 Mon Sep 17 00:00:00 2001
From: Kjartan Oli Agustsson <kjartanoli@outlook.com>
Date: Wed, 18 Jun 2025 16:37:20 +0000
Subject: [PATCH] gnu: ciri-long: Run guix style

* gnu/packages/bioinformatics.scm (ciri-long): Run guix style.

Change-Id: I97e5bd025474ea4ba4f2781f523bc7f5c38fb8e8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
---
 gnu/packages/bioinformatics.scm | 73 ++++++++++++++++-----------------
 1 file changed, 36 insertions(+), 37 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 763a6923a620c5a621542f4d4bd0117e425801f9..53a7bdcfa80d42dcdfcfe7fe5ad786b1d1cdfcc7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4707,47 +4707,46 @@ consensus sequences.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi"))
+        (base32 "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi"))
        ;; Delete bundled binary
        (snippet '(delete-file "libs/ccs"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.py"
-               (("'argparse[^']*',") "") ; only for python2
-               (("==") ">="))))
-         (add-before 'build 'build-libssw
-           (lambda _
-             (with-directory-excursion "libs/striped_smith_waterman"
-               (invoke "make" "libssw.so"))))
-         (add-before 'build 'fix-reference-to-ccs
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "CIRI_long/pipeline.py"
-               (("'ccs -i")
-                (string-append "'"
-                               (assoc-ref inputs "circtools") "/bin/ccs"
-                               " -i")))
-             ;; yuck!
-             (substitute* "CIRI_long/main.py"
-               (("os.chmod\\(lib_path.*") "")))))))
-    (inputs
-     (list circtools
-           python-biopython
-           python-bwapy
-           python-levenshtein
-           python-mappy
-           python-numpy
-           python-pandas
-           python-pysam
-           python-pyspoa
-           python-scikit-learn
-           python-scipy))
-    (native-inputs
-     (list python-cython python-nose python-setuptools))
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'relax-requirements
+                    (lambda _
+                      (substitute* "setup.py"
+                        (("'argparse[^']*',")
+                         "") ;only for python2
+                        (("==")
+                         ">="))))
+                  (add-before 'build 'build-libssw
+                    (lambda _
+                      (with-directory-excursion "libs/striped_smith_waterman"
+                        (invoke "make" "libssw.so"))))
+                  (add-before 'build 'fix-reference-to-ccs
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (substitute* "CIRI_long/pipeline.py"
+                        (("'ccs -i")
+                         (string-append "'"
+                                        (assoc-ref inputs "circtools")
+                                        "/bin/ccs" " -i")))
+                      ;; yuck!
+                      (substitute* "CIRI_long/main.py"
+                        (("os.chmod\\(lib_path.*")
+                         "")))))))
+    (inputs (list circtools
+                  python-biopython
+                  python-bwapy
+                  python-levenshtein
+                  python-mappy
+                  python-numpy
+                  python-pandas
+                  python-pysam
+                  python-pyspoa
+                  python-scikit-learn
+                  python-scipy))
+    (native-inputs (list python-cython python-nose python-setuptools))
     (home-page "https://ciri-cookbook.readthedocs.io/")
     (synopsis "Circular RNA identification for Nanopore sequencing")
     (description "CIRI-long is a package for circular RNA identification using