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32/47: gnu: cnvkit: Update to 0.9.10.
From: |
guix-commits |
Subject: |
32/47: gnu: cnvkit: Update to 0.9.10. |
Date: |
Wed, 10 Jan 2024 13:53:24 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit babc8e58ebaad07b439dc698e0dcc7eb00a01876
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Jan 9 13:14:21 2024 +0100
gnu: cnvkit: Update to 0.9.10.
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.
Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
---
gnu/packages/bioinformatics.scm | 14 +++-----------
1 file changed, 3 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b73a6f67f0..89bc519d68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17848,7 +17848,7 @@ polymorphisms) and indels with respect to a reference
genome and more.")
(define-public cnvkit
(package
(name "cnvkit")
- (version "0.9.9")
+ (version "0.9.10")
(source
(origin
(method git-fetch)
@@ -17857,17 +17857,8 @@ polymorphisms) and indels with respect to a reference
genome and more.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1"))))
+ (base32 "0r303pqjg70zpxa564bavbfj99c6di0dafgqqwx2vh4vfsiif94q"))))
(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
@@ -17882,6 +17873,7 @@ polymorphisms) and indels with respect to a reference
genome and more.")
python-scipy
;; R packages
r-dnacopy))
+ (inputs (list r-minimal)) ;for tests
(home-page "https://cnvkit.readthedocs.org/")
(synopsis "Copy number variant detection from targeted DNA sequencing")
(description
- 19/47: gnu: python-kiwisolver: Update to 1.4.5., (continued)
- 19/47: gnu: python-kiwisolver: Update to 1.4.5., guix-commits, 2024/01/10
- 44/47: gnu: python-metpy: Update to 1.6.0., guix-commits, 2024/01/10
- 31/47: gnu: python-reportlab: Update to 4.0.8., guix-commits, 2024/01/10
- 25/47: gnu: python-cleanlab: Disable test_aux_inputs, enable other tests., guix-commits, 2024/01/10
- 02/47: gnu: Add pybind11-2.10., guix-commits, 2024/01/10
- 09/47: gnu: python-lazy-loader: Update to 0.3., guix-commits, 2024/01/10
- 12/47: gnu: python-afdko: Disable failing test., guix-commits, 2024/01/10
- 18/47: gnu: Add python-cppy., guix-commits, 2024/01/10
- 15/47: gnu: python-scikit-learn: Update to 1.3.2., guix-commits, 2024/01/10
- 35/47: gnu: python-pint: Update to 0.23., guix-commits, 2024/01/10
- 32/47: gnu: cnvkit: Update to 0.9.10.,
guix-commits <=
- 41/47: gnu: python-hicmatrix: Update to 17.1., guix-commits, 2024/01/10
- 37/47: gnu: python-cartopy: Update to 0.22.0., guix-commits, 2024/01/10
- 29/47: gnu: python-pyani: Disable tests., guix-commits, 2024/01/10
- 33/47: gnu: python-plastid: Update to 0.6.1., guix-commits, 2024/01/10
- 21/47: gnu: python-matplotlib: Update to 3.8.2., guix-commits, 2024/01/10
- 39/47: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/10
- 47/47: gnu: python-click-default-group: Update to 1.2.4., guix-commits, 2024/01/10
- 07/47: gnu: python-scipy: Update to 1.11.4., guix-commits, 2024/01/10
- 36/47: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/10
- 27/47: gnu: python-captum: Update to 0.7.0., guix-commits, 2024/01/10