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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-toolkit/package.py | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py new file mode 100644 index 0000000000..876b9ac80d --- /dev/null +++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py @@ -0,0 +1,65 @@ +############################################################################## +# 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') |