kentutils: update to @459, update download location & deps (#42448)

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

var/spack/repos/builtin/packages/kentutils/package.py

@@ -9,26 +9,33 @@
 class Kentutils(MakefilePackage):
     """Jim Kent command line bioinformatic utilities"""
 
-    homepage = "https://github.com/ENCODE-DCC/kentUtils"
-    git = "https://github.com/ENCODE-DCC/kentUtils.git"
+    homepage = "https://genome.cse.ucsc.edu/"
+    url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v453.src.tgz"
 
-    version("302.1", commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9")
+    version("459", sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb")
+    # The above archive only goes back to v305. v302 is left for now but deprecated. Suggest
+    # this is dropped on next update (v302 is from 2014!) and the `requires()` removed.
+    version(
+        "302.1",
+        commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9",
+        git="https://github.com/ENCODE-DCC/kentUtils.git",
+        deprecated=True,
+    )
 
     depends_on("libpng")
     depends_on("openssl")
-
-    # Actually depends on mysql, but mariadb works for now until mysql is
-    # available
+    depends_on("libuuid")
     depends_on("mariadb")
+    depends_on("zlib-api")
+    depends_on("freetype")
+    depends_on("libiconv")
 
-    conflicts("%cce")
-    conflicts("%apple-clang")
-    conflicts("%clang")
-    conflicts("%intel")
-    conflicts("%nag")
-    conflicts("%pgi")
-    conflicts("%xl")
-    conflicts("%xl_r")
+    requires("%gcc", when="@302.1")
+
+    def flag_handler(self, name, flags):
+        if name == "ldflags":
+            flags.append(f'{self.spec["libiconv"].libs.ld_flags}')
+        return (flags, None, None)
 
     def install(self, spec, prefix):
         install_tree("bin", prefix.bin)