From b5d578a5e183f88ba48b73d2271c95ea49a6567a Mon Sep 17 00:00:00 2001
From: Levi Baber <baberlevi@gmail.com>
Date: Mon, 14 May 2018 11:10:19 -0500
Subject: [PATCH] Aegean: new package (#8113)

* aegean: new package

* genometools: set dependent env for aegean
---
 .../repos/builtin/packages/aegean/package.py  | 43 +++++++++++++++++++
 .../builtin/packages/genometools/package.py   |  3 ++
 2 files changed, 46 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/aegean/package.py

diff --git a/var/spack/repos/builtin/packages/aegean/package.py b/var/spack/repos/builtin/packages/aegean/package.py
new file mode 100644
index 0000000000..8ec71982e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aegean/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 Aegean(MakefilePackage):
+    """The AEGeAn Toolkit is designed for the Analysis and Evaluation of
+       Genome Annotations. The toolkit includes a variety of analysis programs
+       as well as a C library whose API provides access to AEGeAn's core
+       functions and data structures."""
+
+    homepage = "http://brendelgroup.github.io/AEGeAn/"
+    url      = "https://github.com/BrendelGroup/AEGeAn/archive/v0.15.2.tar.gz"
+
+    version('0.15.2', 'd7d73f5f132ff52340975b636564e949')
+
+    depends_on('genometools')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('/usr/local', prefix)
diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py
index e08a97b9b4..86e092e7b0 100644
--- a/var/spack/repos/builtin/packages/genometools/package.py
+++ b/var/spack/repos/builtin/packages/genometools/package.py
@@ -43,3 +43,6 @@ class Genometools(MakefilePackage):
 
     def install(self, spec, prefix):
         make('install', 'prefix=%s' % prefix)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('CPATH', self.prefix.include.genometools)