a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
72 lines
2.8 KiB
Python
72 lines
2.8 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Isescan(Package):
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"""A python pipeline to identify IS (Insertion Sequence) elements in
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genome and metagenome"""
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homepage = "https://github.com/xiezhq/ISEScan"
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url = "https://github.com/xiezhq/ISEScan/archive/v1.7.2.1.tar.gz"
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version('1.7.2.1', sha256='b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d')
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depends_on('python@3.3.3:', type='run')
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depends_on('py-numpy@1.8.0:', type='run')
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depends_on('py-scipy@0.13.1:', type='run')
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depends_on('py-biopython@1.62:', type='run')
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depends_on('py-fastcluster', type='run')
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depends_on('py-argparse', type='run')
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depends_on('blast-plus@2.2.31:', type='run')
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depends_on('fraggenescan@1.30:', type='run')
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depends_on('hmmer@3.1b2:', type='run')
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def setup_run_environment(self, env):
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env.prepend_path('PATH', self.prefix)
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env.prepend_path('LD_LIBRARY_PATH',
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join_path(self.prefix, 'ssw201507'))
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def install(self, spec, prefix):
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# build bundled SSW library
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with working_dir('ssw201507'):
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Executable(spack_cc)(
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'-O3', '-pipe', self.compiler.cc_pic_flag, '-shared',
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'-rdynamic', '-o', 'libssw.' + dso_suffix, 'ssw.c', 'ssw.h',
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)
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# set paths to required programs
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blast_pfx = self.spec['blast-plus'].prefix.bin
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blastn_path = blast_pfx.blastn
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blastp_path = blast_pfx.blastp
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makeblastdb_path = blast_pfx.makeblastdb
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hmmer_pfx = self.spec['hmmer'].prefix.bin
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phmmer_path = hmmer_pfx.phmmer
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hmmsearch_path = hmmer_pfx.hmmsearch
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fgs_pfx = self.spec['fraggenescan'].prefix.bin
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fgs_path = join_path(fgs_pfx, 'run_FragGeneScan.pl')
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constants = FileFilter('constants.py')
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constants.filter('/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl',
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fgs_path, string=True)
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constants.filter('/apps/inst/hmmer-3.3/bin/phmmer',
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phmmer_path, string=True)
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constants.filter('/apps/inst/hmmer-3.3/bin/hmmsearch',
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hmmsearch_path, string=True)
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constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastn',
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blastn_path, string=True)
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constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastp',
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blastp_path, string=True)
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constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb',
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makeblastdb_path, string=True)
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# install the whole tree
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install_tree('.', prefix)
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set_executable(join_path(prefix, 'isescan.py'))
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