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-rw-r--r-- | var/spack/repos/builtin/packages/isescan/package.py | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/isescan/package.py b/var/spack/repos/builtin/packages/isescan/package.py new file mode 100644 index 0000000000..1d4b607046 --- /dev/null +++ b/var/spack/repos/builtin/packages/isescan/package.py @@ -0,0 +1,71 @@ +# Copyright 2013-2020 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')) |