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| -rw-r--r-- | var/spack/repos/builtin/packages/portcullis/package.py | 73 |
1 files changed, 73 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py new file mode 100644 index 0000000000..24ec56fdc3 --- /dev/null +++ b/var/spack/repos/builtin/packages/portcullis/package.py @@ -0,0 +1,73 @@ +############################################################################## +# 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/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 * + + +class Portcullis(AutotoolsPackage): + """PORTable CULLing of Invalid Splice junctions""" + + homepage = "https://github.com/maplesond/portcullis" + url = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz" + + version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749') + + depends_on('autoconf@2.53:', type='build') + depends_on('automake@1.11:', type='build') + depends_on('libtool@2.4.2:', type='build') + depends_on('m4', type='build') + + depends_on('zlib', type='build') + depends_on('samtools', type='build') + + depends_on('python@3.4:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-pandas', type=('build', 'run')) + + # later versions of py-sphinx don't get detected by the configure script + depends_on('py-sphinx@1.3:1.4') + + def patch(self): + # remove static linking to libstdc++ + filter_file( + 'AM_LDFLAGS="-static-libstdc++"', + 'AM_LDFLAGS=""', + 'configure.ac', string=True + ) + + # prevent install scripts from ruining our PYTHONPATH + filter_file( + 'export PYTHONPATH=$(DESTDIR)$(pythondir)', + 'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"', + 'scripts/Makefile.am', string=True + ) + + def build(self, spec, prefix): + # build manpages + make('man') + + # run boost build script + sh = which('sh') + sh('build_boost.sh') |