add relion package (#4020)

* add relion package

* fix flake8

* add licence

1 files changed, 62 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py
new file mode 100644
index 0000000000..cd45a14890
--- /dev/null
+++ b/var/spack/repos/builtin/packages/relion/package.py
@@ -0,0 +1,62 @@
+##############################################################################
+# 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 Relion(CMakePackage):
+    """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
+    stand-alone computer program that employs an empirical Bayesian approach to
+    refinement of (multiple) 3D reconstructions or 2D class averages in
+    electron cryo-microscopy (cryo-EM)."""
+
+    homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion"
+    url      = "https://github.com/3dem/relion/archive/2.0.3.tar.gz"
+
+    version('2.0.3', 'c61be5ef00848806278b341f43893f5d')
+
+    variant('gui', default=True, description="build the gui")
+    variant('cuda', default=False, description="enable compute on gpu")
+    variant('double', default=False, description="double precision (cpu) code")
+    variant('double-gpu', default=False, description="double precision (gpu) code")
+
+    depends_on('mpi')
+    depends_on('fftw+float+double')
+    depends_on('fltk', when='+gui')
+    depends_on('cuda', when='+cuda')
+
+    def cmake_args(self):
+        args = [
+            '-DCMAKE_C_FLAGS=-g',
+            '-DCMAKE_CXX_FLAGS=-g',
+            '-DGUI=%s' % ('+gui' in self.spec),
+            '-DDoublePrec_CPU=%s' % ('+double' in self.spec),
+            '-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec),
+        ]
+        if '+cuda' in self.spec:
+            args += [
+                '-DCUDA=on',
+                '-DCUFFT=on',
+            ]
+        return args