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# Copyright 2013-2022 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 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/v1.7.2.1.tar.gz"
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('py-argparse', 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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