Add a package for tophat (#4698)

Lightly tested on CentOS 7.

1 files changed, 47 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py
new file mode 100644
index 0000000000..116db56b32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tophat/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# 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 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 Tophat(AutotoolsPackage):
+    """Spliced read mapper for RNA-Seq."""
+
+    homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
+    url      = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
+
+    version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('boost@1.47:')
+    depends_on('bowtie2', type='run')
+
+    parallel = False
+
+    def configure_args(self):
+        return ["--with-boost={0}".format(self.spec['boost'].prefix)]