From 8084e3bdb3c22b735d3e8df282a3bcb0a7ca6a59 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 20 Sep 2022 14:26:15 +0200
Subject: gnu: python-pyvcf: Update to 0.6.8-0.476169c.

* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
---
 gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++--------------------
 1 file changed, 37 insertions(+), 35 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d35e86cd3e..f54ac6ffab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15541,47 +15541,49 @@ for the analysis and visualization of raw nanopore signal.")
     (license license:mpl2.0)))
 
 (define-public python-pyvcf
-  (package
-    (name "python-pyvcf")
-    (version "0.6.8")
-    ;; Use git, because the PyPI tarballs lack test data.
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
+  (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+        (revision "0"))
+    (package
+      (name "python-pyvcf")
+      (version (git-version "0.6.8" revision commit))
+      ;; Use git, because the PyPI tarballs lack test data.
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
                (url "https://github.com/jamescasbon/PyVCF.git")
                ;; Latest release is not tagged.
-               (commit "bfcedb9bad1a14074ac4526ffdb610611e073810")))
-        (file-name (git-file-name name version))
-        (sha256
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
           (base32
-            "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-        (modify-phases %standard-phases
-          (add-after 'unpack 'patch-sample-script
-            (lambda _
-              ;; Add Python 3 compatibility to this sample script.
-              (substitute* "scripts/vcf_sample_filter.py"
-                (("print (.*)\n" _ arg)
-                 (string-append "print(" arg ")\n")))))
-          (add-after 'install 'remove-installed-tests
-            ;; Do not install test files.
-            (lambda* (#:key inputs outputs #:allow-other-keys)
-              (delete-file-recursively (string-append
+           "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
+      (build-system python-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'patch-sample-script
+             (lambda _
+               ;; Add Python 3 compatibility to this sample script.
+               (substitute* "scripts/vcf_sample_filter.py"
+                 (("print (.*)\n" _ arg)
+                  (string-append "print(" arg ")\n")))))
+           (add-after 'install 'remove-installed-tests
+             ;; Do not install test files.
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (delete-file-recursively (string-append
                                          (site-packages inputs outputs)
                                          "/vcf/test")))))))
-    (native-inputs
-     ;; Older setuptools is needed for use_2to3.
-     (list python-cython python-setuptools-for-tensorflow))
-    (propagated-inputs
-     (list python-pysam python-rpy2))
-    (home-page "https://github.com/jamescasbon/PyVCF")
-    (synopsis "Variant Call Format parser for Python")
-    (description "This package provides a @acronym{VCF,Variant Call Format}
+      (native-inputs
+       ;; Older setuptools is needed for use_2to3.
+       (list python-cython python-setuptools-for-tensorflow))
+      (propagated-inputs
+       (list python-pysam python-rpy2))
+      (home-page "https://github.com/jamescasbon/PyVCF")
+      (synopsis "Variant Call Format parser for Python")
+      (description "This package provides a @acronym{VCF,Variant Call Format}
 parser for Python.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public nanosv
   (package
-- 
cgit v1.2.3