Add package for primer3 (#4615)

* Add package for primer3

Built and mildly tested on CentOS 7.

* Convert to MakefilePackage

I always forget about this...

* Set build_directory the easy way

Life's not always complicated.  Don't go out of my way
to make it so....

* Fix Flake8 issue

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py
new file mode 100644
index 0000000000..fbed680b33
--- /dev/null
+++ b/var/spack/repos/builtin/packages/primer3/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 Primer3(MakefilePackage):
+    """Primer3 is a widely used program for designing PCR primers
+       (PCR = "Polymerase Chain Reaction"). PCR is an essential and
+       ubiquitous tool in genetics and molecular biology. Primer3
+       can also design hybridization probes and sequencing primers."""
+
+    homepage = "http://primer3.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/primer3/files/primer3/2.3.7/primer3-2.3.7.tar.gz/download"
+
+    version('2.3.7', 'c6b89067bf465e62b6b1fd830b5b4418')
+
+    build_directory = 'src'
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdirp(prefix.bin)
+            for binary in ('primer3_core', 'ntdpal', 'oligotm',
+                           'long_seq_tm_test'):
+                install(binary, prefix.bin)