summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorYifan Zhu <ifanzhu@foxmail.com>2018-06-04 13:22:47 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2018-06-04 13:22:47 -0500
commitfcfcd7689a40a387b2e92bbc99571c6a524e53b1 (patch)
tree698e0fa386b453ec5d8ae6ae53d256d65f60545c
parent3144eb40399f681c12861818617ecbf8799cfcc8 (diff)
downloadspack-fcfcd7689a40a387b2e92bbc99571c6a524e53b1.tar.gz
spack-fcfcd7689a40a387b2e92bbc99571c6a524e53b1.tar.bz2
spack-fcfcd7689a40a387b2e92bbc99571c6a524e53b1.tar.xz
spack-fcfcd7689a40a387b2e92bbc99571c6a524e53b1.zip
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
-rw-r--r--var/spack/repos/builtin/packages/phast/package.py58
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)