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
44 lines
1.9 KiB
Python
44 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 RnaSeqc(Package):
|
|
"""RNA-SeQC is a java program which computes a series of quality control
|
|
metrics for RNA-seq data."""
|
|
|
|
homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
|
|
url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
|
|
|
|
version('1.1.8', sha256='0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793', expand=False)
|
|
version('1.1.7', sha256='78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3', expand=False)
|
|
version('1.1.6', sha256='76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6', expand=False)
|
|
version('1.1.5', sha256='1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9', expand=False)
|
|
version('1.1.4', sha256='eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6', expand=False)
|
|
|
|
depends_on('jdk@8:', type='run')
|
|
|
|
def install(self, spec, prefix):
|
|
mkdirp(prefix.bin)
|
|
jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted)
|
|
install(jar_file, 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__), "rna-seqc.sh")
|
|
script = join_path(prefix.bin, "rna-seqc")
|
|
install(script_sh, script)
|
|
set_executable(script)
|
|
|
|
# Munge the helper script to explicitly point to java and the
|
|
# jar file.
|
|
java = self.spec['jdk'].prefix.bin.java
|
|
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
|
|
filter_file('^java', java, script, **kwargs)
|
|
filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file),
|
|
script, **kwargs)
|