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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)
from spack.package import *
class Mixcr(Package):
"""MiXCR is a universal framework that processes big immunome data from
raw sequences to quantitated clonotypes. MiXCR efficiently handles
paired- and single-end reads, considers sequence quality, corrects PCR
errors and identifies germline hypermutations. The software supports
both partial- and full-length profiling and employs all available RNA or
DNA information, including sequences upstream of V and downstream of J
gene segments."""
homepage = "https://mixcr.readthedocs.io/en/master/index.html"
url = "https://github.com/milaboratory/mixcr/releases/download/v3.0.2/mixcr-3.0.2.zip"
version("4.3.2", sha256="8f67cda8e55eeee66b46db0f33308418b6ddb63ca8914623035809ccb5aae2c2")
version("3.0.2", sha256="b4dcad985053438d5f5590555f399edfbd8cb514e1b9717620ee0ad0b5eb6b33")
depends_on("java@8:")
def install(self, spec, prefix):
install_tree(".", prefix)
def setup_run_environment(self, env):
env.prepend_path("PATH", self.prefix)
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