gnu: bedops: Update to 2.4.41.

* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41.
[arguments]: Remove trailing #T from build phases; do not set BINDIR in
make-flags; set CC; replace 'install phase.
[native-inputs]: Add diffutils, perl, and which.

gnu/packages/bioinformatics.scm

@@ -364,7 +364,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 (define-public bedops
   (package
     (name "bedops")
-    (version "2.4.35")
+    (version "2.4.41")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -373,13 +373,18 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
+                "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f
-       #:make-flags (list (string-append "BINDIR=" %output "/bin"))
+     (list
+      ;; We cannot run the tests because the build system makes strange
+      ;; assumptions about where executables are located.
+      #:tests? #false
+      #:test-target "tests"
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target)))
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'unpack-tarballs
             (lambda _
               ;; FIXME: Bedops includes tarballs of minimally patched upstream
@@ -403,9 +408,14 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
                 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
                 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
               (substitute* "third-party/zlib-1.2.7/Makefile.in"
-               (("^SHELL=.*$") "SHELL=bash\n"))
-             #t))
-         (delete 'configure))))
+                (("^SHELL=.*$") "SHELL=bash\n"))))
+          (delete 'configure)
+          (replace 'install
+            (lambda _
+              (invoke "make" "install"
+                      (string-append "BINDIR=" #$output "/bin")))))))
+    (native-inputs
+     (list diffutils perl which))
     (home-page "https://github.com/bedops/bedops")
     (synopsis "Tools for high-performance genomic feature operations")
     (description