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# Copyright 2013-2018 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 *
class Fastqc(Package):
"""A quality control tool for high throughput sequence data."""
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')
depends_on('java', type='run')
depends_on('perl') # for fastqc "script", any perl will do
patch('fastqc.patch', level=0)
def install(self, spec, prefix):
mkdir(prefix.bin)
mkdir(prefix.lib)
install('fastqc', prefix.bin)
for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
install(j, prefix.lib)
for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
install_tree(d, join_path(prefix.lib, d))
chmod = which('chmod')
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.
def setup_environment(self, spack_env, run_env):
"""Add <prefix> to the path; the package has a script at the
top level.
"""
run_env.prepend_path('PATH', self.spec['java'].prefix.bin)
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