mrtrix3: new package (#5568)

* mrtrix3: new package

* specifying conflict dependency ve

var/spack/repos/builtin/packages/mrtrix3/package.py

@@ -0,0 +1,62 @@
+##############################################################################
+# 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/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 *
+import distutils.dir_util
+
+
+class Mrtrix3(Package):
+    """MRtrix provides a set of tools to perform various advanced diffusion MRI
+       analyses, including constrained spherical deconvolution (CSD),
+       probabilistic tractography, track-density imaging, and apparent fibre
+       density."""
+
+    homepage = "http://www.mrtrix.org/"
+    url      = "https://github.com/MRtrix3/mrtrix3"
+
+    version('2017-09-25', commit='72aca89e3d38c9d9e0c47104d0fb5bd2cbdb536d',
+            git='https://github.com/MRtrix3/mrtrix3.git')
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('mesa-glu')
+    depends_on('qt+opengl@4.7:')
+    depends_on('eigen')
+    depends_on('zlib')
+    depends_on('libtiff')
+    depends_on('fftw')
+
+    conflicts('%gcc@7:', when='@2017-09-25')  # MRtrix3/mrtrix3#1041
+
+    def install(self, spec, prefix):
+        configure = Executable('./configure')
+        build = Executable('./build')
+        configure()
+        build()
+        # install_tree('.', prefix) does not work since the prefix
+        # directory already exists by this point
+        distutils.dir_util.copy_tree('.', prefix)
+
+    def setup_environment(self, spac_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)