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ncbitoolkit: Create new package. (#8591)

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* ncbitoolkit: Create new package.

* Fix Flake8 Error.

* Add version constraints and change format.

* Fix version constraints.
This commit is contained in:
lingnanyuan 2018-07-05 21:34:38 -05:00 committed by Adam J. Stewart
parent f8f3fe5b8f
commit 1fa2212543
1 changed files with 65 additions and 0 deletions
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var/spack/repos/builtin/packages/ncbi-toolkit/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2018, 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 NcbiToolkit(AutotoolsPackage):
"""NCBI C++ Toolkit"""
homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--21_0_0.tar.gz"
version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098')
depends_on('boost@1.35.0:')
depends_on('bzip2')
depends_on('libjpeg')
depends_on('libpng')
depends_on('libtiff')
depends_on('libxml2')
depends_on('libxslt@1.1.14:')
depends_on('lzo')
depends_on('pcre')
depends_on('giflib')
depends_on('sqlite@3.6.6:')
depends_on('zlib')
depends_on('samtools')
depends_on('bamtools')
def configure_args(self):
return ['--without-sybase', '--without-fastcgi']
def patch(self):
with working_dir(join_path('src', 'util', 'image')):
filter_file(r'jpeg_start_compress(&cinfo, true)',
'jpeg_start_compress(&cinfo, TRUE)',
'image_io_jpeg.cpp', string=True)
def build(self, spec, prefix):
CompilerVersion = self.compiler.version.joined
with working_dir(join_path(
'GCC{0}-DebugMT64'.format(CompilerVersion), 'build')):
make('all_r')