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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 SspaceLongread(Package):
"""SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled
contigs using long reads
Note: A manual download is required for SSPACE-LongRead.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
https://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread"
manual_download = True
version("1.1", md5="0bb5d8603d7ead4ff1596135a520cc26")
depends_on("perl", type=("build", "run"))
def url_for_version(self, version):
return "file://{0}/40SSPACE-LongRead_v{1}.tar.gz".format(os.getcwd(), version.dashed)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("blasr", prefix.bin)
install("SSPACE-LongRead.pl", prefix.bin)
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