summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorLevi Baber <baberlevi@gmail.com>2018-10-09 12:26:46 -0500
committerGitHub <noreply@github.com>2018-10-09 12:26:46 -0500
commitf12b42e8e637cb18b8e31d2d3752865b70498296 (patch)
tree9b3e4545fe15be77fd2f4351eb99aaf96853c388
parent817ee344c565768d94a2a1dfa307f87c0629e709 (diff)
downloadspack-f12b42e8e637cb18b8e31d2d3752865b70498296.tar.gz
spack-f12b42e8e637cb18b8e31d2d3752865b70498296.tar.bz2
spack-f12b42e8e637cb18b8e31d2d3752865b70498296.tar.xz
spack-f12b42e8e637cb18b8e31d2d3752865b70498296.zip
Autofact: new package (#9317)
* autofact: new package * autofact: typo * autofact: syntax * autofact: deps * autofact: perl mods path * autofact: edit->patch and script path
-rw-r--r--var/spack/repos/builtin/packages/autofact/package.py55
1 files changed, 55 insertions, 0 deletions
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)