From 393fc3261e12bcf4f0eeb2575d5bee4b605a9716 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 20 Sep 2017 17:12:52 -0500 Subject: [PATCH] orthomcl: new package (#5345) Add orthocml package and fix mariadb url --- .../repos/builtin/packages/mariadb/package.py | 4 +- .../builtin/packages/orthomcl/package.py | 49 +++++++++++++++++++ 2 files changed, 51 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/orthomcl/package.py diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index 35ef491eb8..7e5750da61 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/orthomcl/package.py b/var/spack/repos/builtin/packages/orthomcl/package.py new file mode 100644 index 0000000000..ac9ab5bb8c --- /dev/null +++ b/var/spack/repos/builtin/packages/orthomcl/package.py @@ -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)