guix_mirror_bot pushed a commit to branch master
in repository guix.
commit ad5929ab7018f57329481f7129ce803278766628
Author: Nicolas Graves <[email protected]>
AuthorDate: Sat Nov 29 20:56:53 2025 +0100
gnu: ciri-long: Replace python-nose by python-pynose.
* gnu/packages/bioinformatics.scm (ciri-long)
[arguments]: Run guix style -S arguments.
[native-inputs]: Replace python-nose by python-pynose.
Change-Id: If028b5e1eb3915019aa6f4798aaf73d4cd13797f
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++--------------------
1 file changed, 29 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9cebbf1b38..0ca3956124 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4896,32 +4896,34 @@ consensus sequences.")
(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
- (("==")
- ">=")
- ;; This package changed names.
- (("python-Levenshtein")
- "levenshtein"))))
- (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.*")
- "")))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("'argparse[^']*',")
+ "") ;only for python2
+ (("==")
+ ">=")
+ ;; This package changed names.
+ (("python-Levenshtein")
+ "levenshtein"))))
+ (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
@@ -4933,7 +4935,7 @@ consensus sequences.")
python-pyspoa
python-scikit-learn
python-scipy))
- (native-inputs (list python-cython python-nose python-setuptools))
+ (native-inputs (list python-cython python-pynose 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
