Merge branch 'master' into staging

1 files changed, 23 insertions, 9 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e189dd7b00..ec4c44ef54 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4470,26 +4470,40 @@ experiments.")
               ;; The PyPi tarball does not contain tests.
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/taoliu/MACS")
+                    (url "https://github.com/macs3-project/MACS")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15"))))
+                "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15"))
+        (modules '((guix build utils)))
+        ;; Remove files generated by Cython
+        (snippet
+         '(begin
+            (for-each (lambda (file)
+                        (let ((generated-file
+                                (string-append (string-drop-right file 3) "c")))
+                          (when (file-exists? generated-file)
+                            (delete-file generated-file))))
+                      (find-files "." "\\.pyx$"))
+            (delete-file "MACS2/IO/CallPeakUnitPrecompiled.c")
+            #t))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (delete 'check)
-         (add-after 'install 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-v"))))))
+         (replace 'check
+           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "-v"))
+             #t)))))
     (inputs
      `(("python-numpy" ,python-numpy)))
     (native-inputs
-     `(("python-pytest" ,python-pytest)))
-    (home-page "https://github.com/taoliu/MACS/")
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/macs3-project/MACS")
     (synopsis "Model based analysis for ChIP-Seq data")
     (description
      "MACS is an implementation of a ChIP-Seq analysis algorithm for