From 3a58a3ef053558bf229530c1792de23ef2651c44 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 9 Jan 2024 13:14:21 +0100
Subject: [PATCH] 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 953a886270..8ae2b249a9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17907,7 +17907,7 @@ (define-public nanopolish
 (define-public cnvkit
   (package
     (name "cnvkit")
-    (version "0.9.9")
+    (version "0.9.10")
     (source
      (origin
        (method git-fetch)
@@ -17916,17 +17916,8 @@ (define-public cnvkit
              (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
@@ -17941,6 +17932,7 @@ (define-public cnvkit
            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