minimap2, py-mappy: change dependency and build on ARM (#12127)

* minimap2: remove py-mappy dependency and build on ARM
py-mappy: Change URL and new version.

* merge py-mappy to minimap2.

* 1. add type in depends_on.
2. remove unneeded which.

var/spack/repos/builtin/packages/minimap2/package.py

@@ -6,9 +6,10 @@
 from spack import *
 
 
-class Minimap2(MakefilePackage):
+class Minimap2(PythonPackage):
     """Minimap2 is a versatile sequence alignment program that aligns DNA or
-       mRNA sequences against a large reference database."""
+       mRNA sequences against a large reference database.
+       Mappy provides a convenient interface to minimap2."""
 
     homepage = "https://github.com/lh3/minimap2"
     url      = "https://github.com/lh3/minimap2/releases/download/v2.2/minimap2-2.2.tar.bz2"
@@ -17,9 +18,18 @@ class Minimap2(MakefilePackage):
     version('2.10', '52b36f726ec00bfca4a2ffc23036d1a2b5f96f0aae5a92fd826be6680c481c20') 
     version('2.2', '5b68e094f4fa3dfbd9b37d5b654b7715')
 
-    depends_on('py-mappy', type=('build', 'run'))
+    conflicts('target=aarch64', when='@:2.10')
-    depends_on('zlib')
+    depends_on('zlib', type='link')
+    depends_on('py-cython', type='build')
 
-    def install(self, spec, prefix):
+    @run_after('install')
+    def install_minimap2(self):
+        make_arg = []
+        if self.spec.satisfies("target=aarch64"):
+            make_arg.extend([
+                'arm_neon=1',
+                'aarch64~1'
+            ])
+        make(*make_arg)
         mkdirp(prefix.bin)
         install('minimap2', prefix.bin)

var/spack/repos/builtin/packages/py-mappy/package.py

@@ -1,17 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class PyMappy(PythonPackage):
-    """Mappy provides a convenient interface to minimap2."""
-
-    homepage = "https://pypi.python.org/pypi/mappy"
-    url      = "https://pypi.io/packages/source/m/mappy/mappy-2.2.tar.gz"
-
-    version('2.2', 'dfc2aefe98376124beb81ce7dcefeccb')
-
-    depends_on('zlib')