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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 Isescan(Package):
"""A python pipeline to identify IS (Insertion Sequence) elements in
genome and metagenome"""
homepage = "https://github.com/xiezhq/ISEScan"
url = "https://github.com/xiezhq/ISEScan/archive/refs/tags/v1.7.2.1.tar.gz"
license("Apache-2.0")
version("1.7.2.3", sha256="90ef6bc660e471347f65864bd3563f769ed4b79b1a932195f353c5e86351ab05")
version("1.7.2.1", sha256="b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d")
depends_on("python@3.3.3:", type="run")
depends_on("py-numpy@1.8.0:", type="run")
depends_on("py-scipy@0.13.1:", type="run")
depends_on("py-biopython@1.62:", type="run")
depends_on("py-fastcluster", type="run")
depends_on("blast-plus@2.2.31:", type="run")
depends_on("fraggenescan@:1.30", type="run")
depends_on("hmmer@3.1b2:", type="run")
def setup_run_environment(self, env):
env.prepend_path("PATH", self.prefix)
env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "ssw201507"))
def install(self, spec, prefix):
# build bundled SSW library
with working_dir("ssw201507"):
Executable(spack_cc)(
"-O3",
"-pipe",
self.compiler.cc_pic_flag,
"-shared",
"-rdynamic",
"-o",
"libssw." + dso_suffix,
"ssw.c",
"ssw.h",
)
# set paths to required programs
blast_pfx = self.spec["blast-plus"].prefix.bin
blastn_path = blast_pfx.blastn
blastp_path = blast_pfx.blastp
makeblastdb_path = blast_pfx.makeblastdb
hmmer_pfx = self.spec["hmmer"].prefix.bin
phmmer_path = hmmer_pfx.phmmer
hmmsearch_path = hmmer_pfx.hmmsearch
fgs_pfx = self.spec["fraggenescan"].prefix.bin
fgs_path = join_path(fgs_pfx, "run_FragGeneScan.pl")
constants = FileFilter("constants.py")
constants.filter("/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl", fgs_path, string=True)
constants.filter("/apps/inst/hmmer-3.3/bin/phmmer", phmmer_path, string=True)
constants.filter("/apps/inst/hmmer-3.3/bin/hmmsearch", hmmsearch_path, string=True)
constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastn", blastn_path, string=True)
constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastp", blastp_path, string=True)
constants.filter(
"/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb", makeblastdb_path, string=True
)
# install the whole tree
install_tree(".", prefix)
set_executable(join_path(prefix, "isescan.py"))
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