New package: phast (#7993)

* adding partially completed recipe for phast. will need clapack as dependency

* try to install phast

* seems to still need CLAPCK

* using CLAPACK instead

* phast: updated

* fixed flake8 error

* phast cannot build with clapack built with external blas?

* phast: depend on clapack built without external blas

* fixed flake8 errors

* phast: updated build_directory

1 files changed, 58 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/phast/package.py b/var/spack/repos/builtin/packages/phast/package.py
new file mode 100644
index 0000000000..2973c8720c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phast/package.py
@@ -0,0 +1,58 @@
+##############################################################################
+# 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 *
+
+
+class Phast(MakefilePackage):
+    """PHAST is a freely available software package for comparative and
+       evolutionary genomics."""
+
+    homepage = "http://compgen.cshl.edu/phast/index.php"
+    url      = "https://github.com/CshlSiepelLab/phast/archive/v1.4.tar.gz"
+
+    version('1.4', '2bc0412ba58ea1f08ba5e12fad43b4c7')
+
+    # phast cannot build with clapack using external blas
+    depends_on('clapack~external-blas')
+
+    build_directory = 'src'
+
+    @property
+    def build_targets(self):
+        targets = ['CLAPACKPATH={0}'.format(self.spec['clapack'].prefix)]
+        return targets
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'make-include.mk')
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'Makefile')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)