diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/fastqc/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqc/package.py | 45 |
1 files changed, 12 insertions, 33 deletions
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py index 9d20805907..bcebd2b4cf 100644 --- a/var/spack/repos/builtin/packages/fastqc/package.py +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -1,30 +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 distutils.dir_util import copy_tree, mkpath -from distutils.file_util import copy_file class Fastqc(Package): @@ -33,6 +12,7 @@ class Fastqc(Package): homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip" + version('0.11.7', '8fead05fa62c5e723f0d2157a9b5fcd4') version('0.11.5', '3524f101c0ab0bae77c7595983170a76') version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d') @@ -42,15 +22,15 @@ class Fastqc(Package): patch('fastqc.patch', level=0) def install(self, spec, prefix): - mkpath(self.prefix.bin) - mkpath(self.prefix.lib) - copy_file('fastqc', self.prefix.bin) + mkdir(prefix.bin) + mkdir(prefix.lib) + install('fastqc', prefix.bin) for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']: - copy_file(j, self.prefix.lib) + install(j, prefix.lib) for d in ['Configuration', 'net', 'org', 'Templates', 'uk']: - copy_tree(d, join_path(self.prefix.lib, d)) + install_tree(d, join_path(prefix.lib, d)) chmod = which('chmod') - chmod('+x', join_path(self.prefix.bin, 'fastqc')) + chmod('+x', prefix.bin.fastqc) # In theory the 'run' dependency on 'jdk' above should take # care of this for me. In practice, it does not. @@ -58,5 +38,4 @@ class Fastqc(Package): """Add <prefix> to the path; the package has a script at the top level. """ - run_env.prepend_path('PATH', join_path(self.spec['java'].prefix, - 'bin')) + run_env.prepend_path('PATH', self.spec['java'].prefix.bin) |