summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorLevi Baber <baberlevi@gmail.com>2017-12-20 21:10:24 -0600
committerTodd Gamblin <tgamblin@llnl.gov>2017-12-20 19:10:24 -0800
commitf2e061debfe99ddfc5a4f08bb2d0ea9fae14e21d (patch)
tree63f86f84fa56f6b10b18ffb388c1cab9be707044
parente5d6f28b4e6763bf5e3f899be2f584eeff7f0d9e (diff)
downloadspack-f2e061debfe99ddfc5a4f08bb2d0ea9fae14e21d.tar.gz
spack-f2e061debfe99ddfc5a4f08bb2d0ea9fae14e21d.tar.bz2
spack-f2e061debfe99ddfc5a4f08bb2d0ea9fae14e21d.tar.xz
spack-f2e061debfe99ddfc5a4f08bb2d0ea9fae14e21d.zip
Feature/fasttree (#6227)
* fasttree: new package * fasttree: better version handling * fixing line length for flake8
-rw-r--r--var/spack/repos/builtin/packages/fasttree/package.py50
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)