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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/express/package.py | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/express/package.py b/var/spack/repos/builtin/packages/express/package.py new file mode 100644 index 0000000000..687213b75b --- /dev/null +++ b/var/spack/repos/builtin/packages/express/package.py @@ -0,0 +1,63 @@ +############################################################################## +# 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/spack/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 * +import os.path +import glob + + +class Express(CMakePackage): + """eXpress is a streaming tool for quantifying the abundances of a set of + target sequences from sampled subsequences.""" + + homepage = "http://bio.math.berkeley.edu/eXpress/" + url = "https://github.com/adarob/eXpress" + + version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79', + git='https://github.com/adarob/eXpress.git') + + depends_on('boost') + depends_on('bamtools') + depends_on('zlib') + + conflicts('%gcc@6.0.0:', when='@2015-11-29') + + def patch(self): + with working_dir('src'): + files = glob.iglob('*.*') + for file in files: + if os.path.isfile(file): + edit = FileFilter(file) + edit.filter('#include <api', '#include <%s' % self.spec[ + 'bamtools'].prefix.include.bamtools.api) + edit = FileFilter('CMakeLists.txt') + # really ugly way to escape the $ in CMakeLists.txt + edit.filter('{CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/' + 'libbamtools.a', '$') + edit.filter('\\$\\$', '%s' % join_path(self.spec[ + 'bamtools'].prefix.lib.bamtools, 'libbamtools.a')) + + def setup_environment(self, spack_env, run_env): + spack_env.prepend_path('CPATH', self.spec[ + 'bamtools'].prefix.include.bamtools) |