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-rw-r--r--var/spack/repos/builtin/packages/minimap2/package.py20
-rw-r--r--var/spack/repos/builtin/packages/py-mappy/package.py17
2 files changed, 15 insertions, 22 deletions
diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py
index e3c0b48dbe..4e17ec4957 100644
--- a/var/spack/repos/builtin/packages/minimap2/package.py
+++ b/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'))
- depends_on('zlib')
+ conflicts('target=aarch64', when='@:2.10')
+ 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)
diff --git a/var/spack/repos/builtin/packages/py-mappy/package.py b/var/spack/repos/builtin/packages/py-mappy/package.py
deleted file mode 100644
index e1dda142aa..0000000000
--- a/var/spack/repos/builtin/packages/py-mappy/package.py
+++ /dev/null
@@ -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')