diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/picard/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/picard/package.py | 60 |
1 files changed, 29 insertions, 31 deletions
diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py index 744479a7f3..86c6cd6e90 100644 --- a/var/spack/repos/builtin/packages/picard/package.py +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -1,29 +1,9 @@ -############################################################################## -# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. # -# 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 -############################################################################## +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack import * -from shutil import copyfile import glob import os.path import re @@ -36,13 +16,25 @@ class Picard(Package): homepage = "http://broadinstitute.github.io/picard/" url = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar" + _urlfmt = "https://github.com/broadinstitute/picard/releases/download/{0}/picard.jar" + _oldurlfmt = 'https://github.com/broadinstitute/picard/releases/download/{0}/picard-tools-{0}.zip' # They started distributing a single jar file at v2.6.0, prior to # that it was a .zip file with multiple .jar and .so files - version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False, - url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar") - version('1.140', '308f95516d94c1f3273a4e7e2b315ec2', - url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip') + version('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False) + version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False) + version('2.17.0', '72cc527f1e4ca6a799ae0117af60b54e', expand=False) + version('2.16.0', 'fed8928b03bb36e355656f349e579083', expand=False) + version('2.15.0', '3f5751630b1a3449edda47a0712a64e4', expand=False) + version('2.13.2', '3d7b33fd1f43ad2129e6ec7883af56f5', expand=False) + version('2.10.0', '96f3c11b1c9be9fc8088bc1b7b9f7538', expand=False) + version('2.9.4', '5ce72af4d5efd02fba7084dcfbb3c7b3', expand=False) + version('2.9.3', '3a33c231bcf3a61870c3d44b3b183924', expand=False) + version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False) + version('2.9.0', 'b711d492f16dfe0084d33e684dca2202', expand=False) + version('2.8.3', '4a181f55d378cd61d0b127a40dfd5016', expand=False) + version('2.6.0', '91f35f22977d9692ce2718270077dc50', expand=False) + version('1.140', '308f95516d94c1f3273a4e7e2b315ec2') depends_on('java@8:', type='run') @@ -57,13 +49,13 @@ class Picard(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "picard.sh") - script = join_path(prefix.bin, "picard") - copyfile(script_sh, script) + script = prefix.bin.picard + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['java'].prefix, 'bin', 'java') + java = self.spec['java'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'), @@ -73,3 +65,9 @@ class Picard(Package): """The Picard docs suggest setting this as a convenience.""" run_env.prepend_path('PICARD', join_path(self.prefix, 'bin', 'picard.jar')) + + def url_for_version(self, version): + if version < Version('2.6.0'): + return self._oldurlfmt.format(version) + else: + return self._urlfmt.format(version) |