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| author | Toyohisa Kameyama <kameyama@riken.jp> | 2019-08-03 09:21:33 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-08-02 19:21:33 -0500 |
| commit | 50b90ed2bfcd407f5313d1aba05a347dda3af3ca (patch) | |
| tree | f285d711bc2afcd8ea4cba0742a1b636d0937310 /var | |
| parent | 0c1496896d446a95369c373caf9c0b709060e2bc (diff) | |
| download | spack-50b90ed2bfcd407f5313d1aba05a347dda3af3ca.tar.gz spack-50b90ed2bfcd407f5313d1aba05a347dda3af3ca.tar.bz2 spack-50b90ed2bfcd407f5313d1aba05a347dda3af3ca.tar.xz spack-50b90ed2bfcd407f5313d1aba05a347dda3af3ca.zip | |
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.
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/minimap2/package.py | 20 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/py-mappy/package.py | 17 |
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') |