A new package: bowtie. (#3837)

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
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+++ b/var/spack/repos/builtin/packages/bowtie/package.py
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+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Bowtie(MakefilePackage):
+    """Bowtie is an ultrafast, memory-efficient short read aligner
+    for short DNA sequences (reads) from next-gen sequencers."""
+
+    homepage = "https://sourceforge.net/projects/bowtie-bio/"
+    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip"
+
+    version('1.2', '6d97f0ea1a65af11d17cc270cfac4af9')
+
+    variant('tbb', default=False, description='Use Intel thread building block')
+
+    depends_on('tbb', when='+tbb')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('CC = .*', 'CC = ' + env['CC'])
+        makefile.filter('CXX = .*', 'CPP = ' + env['CXX'])
+
+    def build(self, spec, prefix):
+        if '+tbb' in spec:
+            make()
+        else:
+            make('NO_TBB=1')
+
+    def install(self, spec, prefix):
+        make('prefix={0}'.format(self.prefix), 'install')