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-rw-r--r--var/spack/repos/builtin/packages/ncbi-toolkit/package.py65
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
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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')