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author | Audrey Thoma <las_thoma15@iastate.edu> | 2017-08-08 16:35:20 -0500 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-08-08 16:35:19 -0500 |
commit | 632323413572c23f72bcd1f40b14421fd152e88a (patch) | |
tree | 1540ff236b347f081fccaa87ebd0f3eee34be716 /var | |
parent | f82fb75aae335aa2b3c869c6e5065fcee7878b01 (diff) | |
download | spack-632323413572c23f72bcd1f40b14421fd152e88a.tar.gz spack-632323413572c23f72bcd1f40b14421fd152e88a.tar.bz2 spack-632323413572c23f72bcd1f40b14421fd152e88a.tar.xz spack-632323413572c23f72bcd1f40b14421fd152e88a.zip |
astral: new package (#5022)
* astral: new package
* simplifying join_path
* adding build phase and changing jdk to java
* forgot to change jdk to java....
Diffstat (limited to 'var')
-rw-r--r-- | var/spack/repos/builtin/packages/astral/astral.sh | 3 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/astral/package.py | 64 |
2 files changed, 67 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/astral/astral.sh b/var/spack/repos/builtin/packages/astral/astral.sh new file mode 100644 index 0000000000..3f530d7f4e --- /dev/null +++ b/var/spack/repos/builtin/packages/astral/astral.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the astral jar file +java $JAVA_ARGS $JAVA_OPTS -jar astral.jar "$@" diff --git a/var/spack/repos/builtin/packages/astral/package.py b/var/spack/repos/builtin/packages/astral/package.py new file mode 100644 index 0000000000..79feeca07a --- /dev/null +++ b/var/spack/repos/builtin/packages/astral/package.py @@ -0,0 +1,64 @@ +############################################################################## +# Copyright (c) 2013-2016, 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 * +import os.path + + +class Astral(Package): + """ASTRAL is a tool for estimating an unrooted species tree given a set of + unrooted gene trees.""" + + homepage = "https://github.com/smirarab/ASTRAL" + url = "https://github.com/smirarab/ASTRAL/archive/v4.10.7.tar.gz" + + version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d') + + depends_on('java', type=('build', 'run')) + + phases = ['build', 'install'] + + def build(self, spec, prefix): + make = Executable('./make.sh') + make() + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install_tree('lib', prefix.tools.lib) + jar_file = 'astral.{v}.jar'.format(v=self.version) + install(jar_file, prefix.tools) + + script_sh = join_path(os.path.dirname(__file__), "astral.sh") + script = prefix.bin.astral + install(script_sh, script) + set_executable(script) + + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('astral.jar', join_path(prefix.tools, jar_file), + script, **kwargs) + + def setup_environment(self, spack_env, run_env): + run_env.set('ASTRAL_HOME', self.prefix.tools) |