Autofact: new package (#9317)

* autofact: new package

* autofact: typo

* autofact: syntax

* autofact: deps

* autofact: perl mods path

* autofact: edit->patch and script path

var/spack/repos/builtin/packages/autofact/package.py

+##############################################################################
+# 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 *
+import glob
+
+
+class Autofact(Package):
+    """An Automatic Functional Annotation and Classification Tool"""
+
+    homepage = "http://megasun.bch.umontreal.ca/Software/AutoFACT.htm"
+    url      = "http://megasun.bch.umontreal.ca/Software/AutoFACT_v3_4.tar"
+
+    version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4')
+
+    depends_on('perl', type='run')
+    depends_on('perl-bio-perl', type='run')
+    depends_on('perl-io-string', type='run')
+    depends_on('perl-lwp', type='run')
+    depends_on('blast-plus', type='run')
+
+    def patch(self):
+        with working_dir('scripts'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+
+    def install(self, spec, prefix):
+        install_tree(self.stage.source_path, prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.scripts)
+        run_env.set('PATH2AUTOFACT', self.prefix)