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# Copyright 2013-2022 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.package import *
class Fastqc(Package):
"""A quality control tool for high throughput sequence data."""
homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
version("0.11.9", sha256="15510a176ef798e40325b717cac556509fb218268cfdb9a35ea6776498321369")
version("0.11.7", sha256="59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112")
version("0.11.5", sha256="dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66")
version("0.11.4", sha256="adb233f9fae7b02fe99e716664502adfec1b9a3fbb84eed4497122d6d33d1fe7")
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_run_environment(self, env):
"""Add <prefix> to the path; the package has a script at the
top level.
"""
env.prepend_path("PATH", self.spec["java"].prefix.bin)
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