soapdenovo-trans: Create new package. (#7649)

* soapdenovo-trans: Create new package.

* change header

* soapdenovo-trans: change package type to makefile.

* soapdenovo-trans: fix flake8 error.

var/spack/repos/builtin/packages/soapdenovo-trans/package.py

@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 SoapdenovoTrans(MakefilePackage):
+    """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
+       SOAPdenovo framework, adapt to alternative splicing and different
+       expression level among transcripts."""
+
+    homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
+    url      = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
+
+    version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter('Makefile')
+            makefile.filter('CFLAGS=         -O3 -fomit-frame-pointer -static',
+                            'CFLAGS=         -O3 -fomit-frame-pointer')
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+            make('127mer=1', parallel=False)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)