Feature/fasttree (#6227)

* fasttree: new package

* fasttree: better version handling

* fixing line length for flake8

1 files changed, 50 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/fasttree/package.py b/var/spack/repos/builtin/packages/fasttree/package.py
new file mode 100644
index 0000000000..d1b0163004
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fasttree/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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/spack/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 Fasttree(Package):
+    """FastTree infers approximately-maximum-likelihood phylogenetic
+       trees from alignments of nucleotide or protein sequences.
+       FastTree can handle alignments with up to a million of sequences
+       in a reasonable amount of time and memory."""
+
+    homepage = "http://www.microbesonline.org/fasttree"
+    url      = "http://www.microbesonline.org/fasttree/FastTree-2.1.10.c"
+
+    version('2.1.10', '1c2c6425a638ec0c61ef064cda687987', expand=False, url='http://www.microbesonline.org/fasttree/FastTree-2.1.10.c')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-O3', self.compiler.openmp_flag,
+           '-DOPENMP', '-finline-functions', '-funroll-loops', '-Wall',
+           '-oFastTreeMP', 'FastTree-' + format(spec.version.dotted) + '.c',
+           '-lm')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('FastTreeMP', prefix.bin)