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# Copyright 2013-2023 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 Cufflinks(Package):
"""Cufflinks assembles transcripts, estimates their abundances, and tests
for differential expression and regulation in RNA-Seq samples."""
homepage = "https://cole-trapnell-lab.github.io/cufflinks"
url = "https://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz"
license("BSL-1.0")
version("2.2.1", sha256="39f812452cae26462e5d2671d38104d9e8ef30aaf9ab6dea8ca57f50f46448e4")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("cuffcompare", prefix.bin)
install("cuffdiff", prefix.bin)
install("cufflinks", prefix.bin)
install("cuffmerge", prefix.bin)
install("cuffnorm", prefix.bin)
install("cuffquant", prefix.bin)
install("gffread", prefix.bin)
install("gtf_to_sam", prefix.bin)
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