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# Copyright 2013-2024 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)
import os
from spack.package import *
class Rnaquast(Package):
"""Quality assessment of de novo transcriptome assemblies from RNA-Seq data
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome
and gene database. In addition, rnaQUAST is also capable of estimating gene
database coverage by raw reads and de novo quality assessment
using third-party software."""
homepage = "https://github.com/ablab/rnaquast"
url = "https://github.com/ablab/rnaquast/archive/refs/tags/v2.2.0.tar.gz"
maintainers("dorton21")
version("2.2.0", sha256="117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334")
depends_on("python@2.5:", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-joblib", type=("build", "run"))
depends_on("py-gffutils", type=("build", "run"))
depends_on("gmap-gsnap", type=("build", "run"))
depends_on("blast-plus", type=("build", "run"))
def install(self, spec, prefix):
install_tree(".", prefix.bin)
os.rename("%s/rnaQUAST.py" % prefix.bin, "%s/rnaQUAST" % prefix.bin)
def setup_run_environment(self, env):
env.prepend_path("PATH", prefix.bin)
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