62927654dd
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
52 lines
1.9 KiB
Python
52 lines
1.9 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
|
|
# Spack Project Developers. See the top-level COPYRIGHT file for details.
|
|
#
|
|
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
|
|
|
from spack import *
|
|
import os.path
|
|
|
|
|
|
class Qorts(RPackage):
|
|
"""The QoRTs software package is a fast, efficient, and portable
|
|
multifunction toolkit designed to assist in the analysis, quality
|
|
control, and data management of RNA-Seq and DNA-Seq datasets. Its
|
|
primary function is to aid in the detection and identification of
|
|
errors, biases, and artifacts produced by high-throughput sequencing
|
|
technology."""
|
|
|
|
homepage = "https://github.com/hartleys/QoRTs"
|
|
url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
|
|
|
|
version('1.2.42', sha256='c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08')
|
|
|
|
depends_on('java', type='run')
|
|
|
|
resource(
|
|
name='QoRTs.jar',
|
|
url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
|
|
sha256='e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce',
|
|
placement='jarfile',
|
|
expand=False
|
|
)
|
|
|
|
@run_after('install')
|
|
def install_jar(self):
|
|
install_tree(join_path(self.stage.source_path, 'jarfile'),
|
|
self.prefix.bin)
|
|
|
|
# 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__), "QoRTs.sh")
|
|
script = self.prefix.bin.QoRTs
|
|
install(script_sh, script)
|
|
set_executable(script)
|
|
|
|
# Munge the helper script to explicitly point to java and the
|
|
# jar file.
|
|
java = self.spec['java'].prefix.bin.java
|
|
kwargs = {'backup': False}
|
|
filter_file('^java', java, script, **kwargs)
|
|
filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
|
|
script, **kwargs)
|