From f12b42e8e637cb18b8e31d2d3752865b70498296 Mon Sep 17 00:00:00 2001 From: Levi Baber Date: Tue, 9 Oct 2018 12:26:46 -0500 Subject: Autofact: new package (#9317) * autofact: new package * autofact: typo * autofact: syntax * autofact: deps * autofact: perl mods path * autofact: edit->patch and script path --- .../repos/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) -- cgit v1.2.3-60-g2f50