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orthomcl: new package (#5345)

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Add orthocml package and fix mariadb url
This commit is contained in:
Audrey Thoma 2017-09-20 17:12:52 -05:00 committed by scheibelp
parent 5267681abe
commit 393fc3261e
2 changed files with 51 additions and 2 deletions
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4
var/spack/repos/builtin/packages/mariadb/package.py
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@ -33,11 +33,11 @@ class Mariadb(CMakePackage):
tools make it very versatile for a wide variety of use cases."""
homepage = "https://mariadb.org/about/"
url = "https://downloads.mariadb.org/f/mariadb-10.1.23/source/mariadb-10.1.23.tar.gz"
url = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz"
version('10.2.8', 'f93cbd5bfde3c0d082994764ff7db580')
version('10.1.23', '1a7392cc05c7c249acd4495022719ca8')
version('5.5.56', '8bc7772fea3e11b0bc1a09d2278e2e32')
# old versions, do not fetch under given url anymore
version('10.1.14', '294925531e0fd2f0461e3894496a5adc')
version('5.5.49', '67b5a499a5f158b2a586e6e3bfb4f304')

49
var/spack/repos/builtin/packages/orthomcl/package.py Normal file
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@ -0,0 +1,49 @@
##############################################################################
# Copyright (c) 2013-2017, 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/llnl/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 Orthomcl(Package):
"""OrthoMCL is a genome-scale algorithm for grouping orthologous protein
sequences."""
homepage = "http://orthomcl.org/orthomcl/"
url = "http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz"
version('2.0.9', '2e0202ed4e36a753752c3567edb9bba9')
depends_on('perl', type=('build', 'run'))
depends_on('blast-plus')
depends_on('mcl')
depends_on('mariadb')
def install(self, spec, prefix):
install_tree('bin', prefix.bin)
install_tree('config', prefix.config)
install_tree('doc', prefix.doc)
install_tree('lib', prefix.lib)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', self.prefix.lib)