From 87c65fafa989b27381bc78addf8e375730217e8a Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 12 Oct 2017 11:07:42 -0500 Subject: minimap2: new package (#5722) --- .../repos/builtin/packages/minimap2/package.py | 41 ++++++++++++++++++++++ .../repos/builtin/packages/py-mappy/package.py | 36 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 var/spack/repos/builtin/packages/minimap2/package.py create mode 100644 var/spack/repos/builtin/packages/py-mappy/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py new file mode 100644 index 0000000000..74835b7950 --- /dev/null +++ b/var/spack/repos/builtin/packages/minimap2/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Minimap2(MakefilePackage): + """Minimap2 is a versatile sequence alignment program that aligns DNA or + mRNA sequences against a large reference database.""" + + homepage = "https://github.com/lh3/minimap2" + url = "https://github.com/lh3/minimap2/releases/download/v2.2/minimap2-2.2.tar.bz2" + + version('2.2', '5b68e094f4fa3dfbd9b37d5b654b7715') + + depends_on('py-mappy', type=('build', 'run')) + + def install(self, spec, prefix): + 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 new file mode 100644 index 0000000000..80dddd10b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mappy/package.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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') -- cgit v1.2.3-60-g2f50