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[bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9.
From: |
Ricardo Wurmus |
Subject: |
[bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9. |
Date: |
Mon, 12 Dec 2022 15:27:16 +0100 |
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
---
gnu/packages/bioinformatics.scm | 21 ++++++++++++++++-----
1 file changed, 16 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8a8ddc361..5e2e0796a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14225,7 +14225,7 @@ (define-public nanopolish
(define-public cnvkit
(package
(name "cnvkit")
- (version "0.9.5")
+ (version "0.9.9")
(source
(origin
(method git-fetch)
@@ -14234,17 +14234,28 @@ (define-public cnvkit
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82"))))
- (build-system python-build-system)
+ (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a
+ (add-after 'unpack 'compatibility
+ (lambda _
+ (substitute* "setup.py"
+ (("'joblib.*") "")))))))
(propagated-inputs
(list python-biopython
python-future
python-matplotlib
python-numpy
- python-reportlab
python-pandas
- python-pysam
+ python-pomegranate
python-pyfaidx
+ python-pysam
+ python-reportlab
+ python-scikit-learn
python-scipy
;; R packages
r-dnacopy))
--
2.36.1
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., (continued)
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., zimoun, 2022/12/12
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., Ricardo Wurmus, 2022/12/12
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., Simon Tournier, 2022/12/12
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., Ricardo Wurmus, 2022/12/12
- [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., Simon Tournier, 2022/12/12
- bug#60009: [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0., Ricardo Wurmus, 2022/12/12
[bug#60009] [PATCH 17/18] gnu: seqmagick: Update to 0.8.4., Ricardo Wurmus, 2022/12/12
[bug#60009] [PATCH 14/18] gnu: python-apispec: Update to 6.0.2., Ricardo Wurmus, 2022/12/12
[bug#60009] [PATCH 15/18] gnu: python-pyjwt: Update to 2.6.0., Ricardo Wurmus, 2022/12/12
[bug#60009] [PATCH 16/18] gnu: python-flasgger: Update to 0.9.5., Ricardo Wurmus, 2022/12/12
[bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9.,
Ricardo Wurmus <=