From f12b42e8e637cb18b8e31d2d3752865b70498296 Mon Sep 17 00:00:00 2001
From: Levi Baber <baberlevi@gmail.com>
Date: Tue, 9 Oct 2018 12:26:46 -0500
Subject: [PATCH] Autofact: new package (#9317)
* autofact: new package
* autofact: typo
* autofact: syntax
* autofact: deps
* autofact: perl mods path
* autofact: edit->patch and script path
---
.../builtin/packages/autofact/package.py | 55 +++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/autofact/package.py
diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py
new file mode 100644
index 0000000000..47038685c4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/autofact/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# 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)
--
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